diff --git a/.circleci/config.yml b/.circleci/config.yml
index cf237bd82639b..81ecb0653c316 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.medium
+    resource_class: arm.large
 
 jobs: # a basic unit of work in a run
   build_and_test:
diff --git a/build-fail-blacklist b/build-fail-blacklist
index a176375749eff..eb572aa005ebc 100644
--- a/build-fail-blacklist
+++ b/build-fail-blacklist
@@ -772,9 +772,6 @@ recipes/perl-gd
 # sha mismatch when downloading source
 recipes/fmlrc2
 
-# tries to download zlib itself, which fails
-recipes/d4binding
-
 # no matching package named `quickersort` found
 recipes/mudskipper
 
diff --git a/recipes/abismal/build.sh b/recipes/abismal/build.sh
index 66d0cf72332e6..69fef46ab9252 100644
--- a/recipes/abismal/build.sh
+++ b/recipes/abismal/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
-./configure --prefix=$PREFIX
-make CXXFLAGS="-O3 -D_LIBCPP_DISABLE_AVAILABILITY"
+
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
+./configure --prefix="$PREFIX"
+
+make CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
 make install
diff --git a/recipes/abismal/meta.yaml b/recipes/abismal/meta.yaml
index 43fa4b6849707..0960ba5728525 100644
--- a/recipes/abismal/meta.yaml
+++ b/recipes/abismal/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.2.3" %}
+{% set version = "3.2.4" %}
 
 package:
   name: abismal
@@ -10,10 +10,9 @@ build:
     # abismal is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('abismal', max_pin="x.x") }}
 
-
 source:
   url: https://github.com/smithlabcode/abismal/releases/download/v{{ version }}/abismal-{{ version }}.tar.gz
-  sha256: 0698ca408feb7e2650468e66dfdd4615e9405f64cd5496272fe2226cefd21322
+  sha256: 822e5efe322f989c561a1fb728bd6f57f49d94033620eb1bc5046f22a8492544
 
 requirements:
   build:
@@ -21,21 +20,26 @@ requirements:
     - {{ compiler('cxx') }}
     - autoconf
     - automake
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
+    - libtool
   host:
     - zlib
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   run:
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
 
 about:
-  home: https://github.com/smithlabcode/abismal
-  license: GPL-3.0-only
+  home: "https://github.com/smithlabcode/abismal"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
   summary: |
-    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads
-  doc_url: 'https://github.com/smithlabcode/abismal/blob/master/docs/MANUAL.md'
+    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads.
+  doc_url: 'https://github.com/smithlabcode/abismal/blob/v{{ version }}/docs/MANUAL.md'
+  dev_url: "https://github.com/smithlabcode/abismal"
 
 test:
   commands:
@@ -45,3 +49,6 @@ extra:
   recipe-maintainers:
     - andrewdavidsmith
     - guilhermesena1
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/abyss/build.sh b/recipes/abyss/build.sh
index fcde870f701e4..519380774dc54 100644
--- a/recipes/abyss/build.sh
+++ b/recipes/abyss/build.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 if [[ "$(uname)" == Darwin ]]; then
     # Fix for install_name_tool error:
     #   error: install_name_tool: changing install names or rpaths can't be
@@ -9,13 +12,14 @@ if [[ "$(uname)" == Darwin ]]; then
     export LDFLAGS="$LDFLAGS -headerpad_max_install_names"
 fi
 
-./configure \
-    --prefix="$PREFIX" \
-    --with-boost="$PREFIX" \
-    --with-mpi="$PREFIX" \
-    --with-sparsehash="$PREFIX" \
-    --without-sqlite || cat config.log
-make AM_CXXFLAGS=-Wall
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include" \
+	--with-boost="${PREFIX}" \
+	--with-mpi="${PREFIX}" \
+	--with-sparsehash="${PREFIX}" \
+	--without-sqlite || cat config.log
+make AM_CXXFLAGS="-Wall" -j"${CPU_COUNT}"
 make install
 
 $RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-pe" "$PREFIX/bin/abyss-pe.Makefile"
diff --git a/recipes/abyss/config.patch b/recipes/abyss/config.patch
deleted file mode 100644
index 0eff6cb938fc6..0000000000000
--- a/recipes/abyss/config.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Upstream release contains config.{guess,sub} from ten years ago that
-don't handle Apple silicon. This patches minimally around it.
-
---- a/config.sub	2014-06-10 20:03:11
-+++ b/config.sub	2024-07-23 19:48:49
-@@ -436,6 +436,9 @@
- 	| ymp-* \
- 	| z8k-* | z80-*)
- 		;;
-+	arm64-apple)
-+		basic_machine=aarch64-apple
-+		;;
- 	# Recognize the basic CPU types without company name, with glob match.
- 	xtensa*)
- 		basic_machine=$basic_machine-unknown
diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml
index 813b1133e843f..d1fc364dca7f9 100644
--- a/recipes/abyss/meta.yaml
+++ b/recipes/abyss/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "abyss" %}
-{% set version = "2.3.9" %}
+{% set version = "2.3.10" %}
  
 package:
   name: {{ name|lower }}
@@ -12,20 +12,22 @@ build:
 
 source:
   url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz
-  sha256: 55f0b27b67b4486dc6cbe132c0f4c228ee4f9e86c56292a7b50633df87e3212e
-  patches:
-    - config.patch
+  sha256: bbe42e00d1ebb53ec6afaad07779baaaee994aa5c65b9a38cf4ad2011bb93c65
 
 requirements:
   build:
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
   host:
     - boost-cpp
     - sparsehash
     - openmpi
     - btllib
   run:
+    - boost-cpp
     - openmpi
     - make
     - util-linux  # [linux]
@@ -38,12 +40,13 @@ test:
     - abyss-pe help | grep -q "Assemble reads into contigs and scaffolds"
 
 about:
-  home: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-  license: GPL-3.0-only
+  home: "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
-  dev_url: https://github.com/bcgsc/abyss
-  doc_url: https://github.com/bcgsc/abyss#readme
+  summary: "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler."
+  dev_url: "https://github.com/bcgsc/abyss"
+  doc_url: "https://github.com/bcgsc/abyss/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
@@ -54,5 +57,6 @@ extra:
     extended-base: true
   identifiers:
     - biotools:abyss
+    - usegalaxy-eu:abyss-pe
     - doi:10.1101/gr.214346.116
     - doi:10.1101/gr.089532.108
diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml
index 0bfcfd3e0e7e6..9d64f383ab285 100644
--- a/recipes/afpdb/meta.yaml
+++ b/recipes/afpdb/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
+  sha256: aad8f90092630dce86254227bc94e4f42a28598a6ccf69f07d0e619bc88c0ae8
 
 build:
   number: 0
diff --git a/recipes/annembed/build.sh b/recipes/annembed/build.sh
index f4634f476014f..169790fc0d311 100644
--- a/recipes/annembed/build.sh
+++ b/recipes/annembed/build.sh
@@ -5,4 +5,4 @@
 export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
-RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX
+RUST_BACKTRACE=1 cargo install --features intel-mkl-static,simdeez_f --verbose --path . --root $PREFIX
diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml
index 8b87e6aa37968..2c4387219f3f6 100644
--- a/recipes/annembed/meta.yaml
+++ b/recipes/annembed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.4" %}
+{% set version = "0.1.6" %}
 
 package:
   name: annembed
@@ -11,7 +11,7 @@ build:
   skip: True  # [osx]
 source:
   url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz
-  sha256: 0f923798db3843aac0352eba5d2b169673ee087fce2cc37981bd19a1ecb878d0
+  sha256: f60dceb94df46ae2ccc7ed228988a67df254a28f02b9b545baf31ca6e85f7f8d
 
 requirements:
   build:
@@ -28,7 +28,7 @@ test:
 about:
   home: https://github.com/jianshu93/annembed
   license: MIT
-  summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data
+  summary: annembed is an ultra-fast and scalable non-linear dimension reduction/embedding algorithm (similar to UMAP or t-SNE) for large-scale biological data
 
 extra:
   maintainers:
diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml
index af993fa78011c..8ea909de74f8d 100644
--- a/recipes/assembly_finder/meta.yaml
+++ b/recipes/assembly_finder/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "assembly_finder" %}
-{% set version = "0.7.7" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02
+  sha256: 8708d9185dccce21808777c79dad1c2b019ca1f416035c2e5e16b0c32928566e
 
 build:
   number: 0
@@ -20,17 +20,17 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.11
     - pip
+    - setuptools
   run:
-    - python >=3.10
-    - mamba >=1.5.8
+    - python >=3.11
     - snakemake-minimal >=8.0.0
     - snaketool-utils >=0.0.5
     - attrmap >=0.0.7
-    - pyyaml >=6.0
+    - pyyaml >=6.0.1
     - pandas >=2.2.1
-    - rich-click >=1.7.4
+    - rich-click >=1.8.3
 
 test:
   commands:
diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml
index ee058b1597a18..f9d27847244f7 100644
--- a/recipes/auspice/meta.yaml
+++ b/recipes/auspice/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.58.0" %}
+{% set version = "2.59.1" %}
 {% set name = "auspice" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz
-  sha256: cb746010b28de5d0232258113820c551f6f4287e5b0ff67a1e5854adc381ac96
+  sha256: 828bc00e27ca3d403332686ab041dd3171c999a1a942b9fe89ba8256daedfecc
 
 build:
   number: 0
@@ -20,14 +20,14 @@ requirements:
     # vary across platforms.
     - "{{ compiler('c') }}"
     - "{{ compiler('cxx') }}"
-    - nodejs 16.*|18.*|20.*
+    - nodejs 16.*|18.*|20.*|22.*
     - python
     - pkg-config
     - yarn 1.*
   host:
     - icu
   run:
-    - nodejs 16.*|18.*|20.*
+    - nodejs 16.*|18.*|20.*|22.*
 
 test:
   commands:
diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml
index f9de466d197cd..24283de93f98a 100644
--- a/recipes/bactopia-py/meta.yaml
+++ b/recipes/bactopia-py/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "bactopia-py" %}
-{% set version = "1.2.1" %}
+{% set version = "1.3.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
-  sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1
+  sha256: ac777d8338823c5709d5d4ad3af719faf7084e4c1956fb108ae3d410ad6f74e8
 
 build:
   noarch: python
@@ -39,6 +39,7 @@ test:
     - bactopia-citations --help
     - bactopia-citations --version
     - bactopia-datasets --help
+    - bactopia-datasets --version
     - bactopia-download --help
     - bactopia-prepare --help
     - bactopia-search --help
diff --git a/recipes/biobb_amber/meta.yaml b/recipes/biobb_amber/meta.yaml
index a83508f495c17..f9ff0871709c2 100644
--- a/recipes/biobb_amber/meta.yaml
+++ b/recipes/biobb_amber/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_amber" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 11fe9767c895c5de4a2e643f1c2de00f57bb03c8e0835415542c98aec2ca6040
+  sha256: 11ce0b1a7f7ec912136d31a46bffdc1c85b831686a51b8e9fe5e35cac611f09c
 
 build:
   number: 0
@@ -18,14 +18,14 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.8,<3.11
     - setuptools
-    - biobb_common ==4.2.0
-    - ambertools >=22.0
+    - biobb_common ==5.0.0
+    - ambertools ==22.5.0
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - ambertools >=22.0
+    - python >=3.8,<3.11
+    - biobb_common ==5.0.0
+    - ambertools ==22.5.0
 
 test:
   imports:
diff --git a/recipes/biobb_analysis/meta.yaml b/recipes/biobb_analysis/meta.yaml
index 8ba9f1efac1b9..c96372e9fe1d3 100644
--- a/recipes/biobb_analysis/meta.yaml
+++ b/recipes/biobb_analysis/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_analysis" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: e42a054bbc9c066d47443a18ee370dd97632f93de32c44aeb586a19bce85aa37
+  sha256: 8bf930ecd4cff6b3ad3a97a92599913225295725056c5369bd0e7f536bb4008d
 
 build:
   number: 0
@@ -18,16 +18,16 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
-    - gromacs ==2022.2
-    - ambertools >=22.0
+    - biobb_common ==5.0.0
+    - gromacs >=2022.2
+    - ambertools >=22.5
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - gromacs ==2022.2
-    - ambertools >=22.0
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - gromacs >=2022.2
+    - ambertools >=22.5
 test:
   imports:
     - biobb_analysis
diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml
index 2e12dae73345e..17755ee4702be 100644
--- a/recipes/biobb_chemistry/meta.yaml
+++ b/recipes/biobb_chemistry/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "4.2.1" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 729e6b3b955ad9e62997a162c58b3e84945b1e8a7a766a158a093ffb0b1388a8
+  sha256: c4f3926a8a219410afa1e79feb84b71a2d1bb70bc0700039d52726853113b0e8
 
 build:
   number: 0
@@ -18,18 +18,18 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.0
-    - acpype ==2022.7.21
+    - ambertools >=22.5
+    - acpype >=2023.10.27
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.0
-    - acpype ==2022.7.21
+    - ambertools >=22.5
+    - acpype >=2023.10.27
 test:
   imports:
     - biobb_chemistry
diff --git a/recipes/biobb_cmip/meta.yaml b/recipes/biobb_cmip/meta.yaml
index d8dbe24de5f7f..44ee15fd3d4ab 100644
--- a/recipes/biobb_cmip/meta.yaml
+++ b/recipes/biobb_cmip/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_cmip" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: c3dd9f0f9da33093f3e13792601048a4d1064d65add8456a4a7baa8e27e3d55d
+  sha256: 4f934f23f7826b5de97fd2ecaaa476a3842d203b6a04ef52b584fa8d81ccd610
 
 build:
   number: 0
@@ -18,18 +18,18 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - cmip ==2.7.0
     - mdanalysis >=2.0.0
-    - biobb_structure_checking ==3.13.4
+    - biobb_structure_checking ==3.13.5
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - cmip ==2.7.0
     - mdanalysis >=2.0.0
-    - biobb_structure_checking ==3.13.4
+    - biobb_structure_checking ==3.13.5
 
 test:
   imports:
diff --git a/recipes/biobb_cp2k/meta.yaml b/recipes/biobb_cp2k/meta.yaml
index 104cb0718f3ac..29c8cae631c5f 100644
--- a/recipes/biobb_cp2k/meta.yaml
+++ b/recipes/biobb_cp2k/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_cp2k" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 17537ebf02ecd2e66406d61da55334c9df4069d4ccaee4b3de4afac9ff622f30
+  sha256: c6b7f13e37b57e228d0a0a5430c40c6c5c892d58d47e4d72c72306dec5339c95
 
 build:
   number: 0
diff --git a/recipes/biobb_dna/meta.yaml b/recipes/biobb_dna/meta.yaml
index 7c781adfcf6f3..bc13f9acbc562 100644
--- a/recipes/biobb_dna/meta.yaml
+++ b/recipes/biobb_dna/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_dna" %}
-{% set version = "4.2.4" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f9343a8ec9ca8b0c9c764657979daf2b06b58ee242d30c2f8679416467d5ada4
+  sha256: 513e133bf3e48ce0e45fb2659182a112798c1e1d8068a8a2fa99d21007af4768
 
 build:
   number: 0
@@ -18,16 +18,16 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - pandas >=1.3.0
     - scikit-learn >=0.24.2
     - curves ==3.0.2
 
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - pandas >=1.3.0
     - scikit-learn >=0.24.2
     - curves ==3.0.2
@@ -51,7 +51,7 @@ about:
     \ [![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_dna)\
     \ [![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_dna)\
     \ [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\
-    \n# biobb_dna\n\n### Introduction\nBiobb_dna is a package composed of different analyses for nucleic acid trajectories. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
+    \n# biobb_dna\n\n### Introduction\nBiobb_dna is a package composed of different analyses for nucleic acid trajectories. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
     \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
diff --git a/recipes/biobb_flexdyn/meta.yaml b/recipes/biobb_flexdyn/meta.yaml
index 4dbcdc7bf02be..04e4803769ec5 100644
--- a/recipes/biobb_flexdyn/meta.yaml
+++ b/recipes/biobb_flexdyn/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_flexdyn" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 5cfe112fb35a86fff4d452efb966fa18757bad4ea1f4017b226e765a8e6f776e 
+  sha256: ae30f8f64e851b1e7546c7c212a079839d1e26cf01fb9d4c88bb0eb1f29f6203
 
 build:
   number: 0
@@ -18,17 +18,19 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9,<3.12
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
+    - sciPy >=1.13.0,<1.14.0
     - concoord
     - prody
     - imods
     - nolb
 
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9,<3.12
+    - biobb_common ==5.0.0
+    - sciPy >=1.13.0,<1.14.0
     - concoord
     - prody
     - imods
@@ -43,8 +45,8 @@ about:
   home: https://github.com/bioexcel/biobb_flexdyn
   license: Apache Software License
   license_family: APACHE
-  summary: Biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins. 
-  description: "# biobb_flexdyn\n\n### Introduction\nBiobb_flexdyn allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
+  summary: Biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.
+  description: "# biobb_flexdyn\n\n### Introduction\nBiobb_flexdyn allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
     \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
diff --git a/recipes/biobb_flexserv/meta.yaml b/recipes/biobb_flexserv/meta.yaml
index a766b6d8ff5cd..285ea0dba28b9 100644
--- a/recipes/biobb_flexserv/meta.yaml
+++ b/recipes/biobb_flexserv/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_flexserv" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 62b3ecb6dacca9cd0496dec9e6ebe5e43e4d0e3fcfd8b122a20dda940d49162e 
+  sha256: 90c2b03541d144026f2f6866e8fd166b0440f73a7c34c83f49b81dd826374edc 
 
 build:
   number: 0
diff --git a/recipes/biocode/meta.yaml b/recipes/biocode/meta.yaml
index 42ff93ce5a92a..4b38fadd27216 100644
--- a/recipes/biocode/meta.yaml
+++ b/recipes/biocode/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biocode" %}
-{% set version = "0.11.0" %}
+{% set version = "0.12.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,19 +7,19 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 5c0df506d07e6b073b56da360bba4dad8e0b90e4ceb6f62009ae51c56a83b162
+  sha256: 42e6713223521337c04e3a7f92e1ae6229c5e00999b05a95a6c20643649475e2
 
 build:
   noarch: python
   number: 0
-  script: "{{ PYTHON }} -m pip install . --no-deps -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 requirements:
   host:
     - pip
     - python >=3.6
-
+    - setuptools
   run:
     - jinja2
     - matplotlib-base
diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
index c8a92fc0b1c12..ffb100d77defe 100644
--- a/recipes/bioconda-utils/meta.yaml
+++ b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.3.2" %}
-{% set sha256 = "6c6dcac689a2fb0f8142546aa9021bfd620fe484e724e4844a2d2e55c337747c" %}
+{% set version = "3.4.0" %}
+{% set sha256 = "ec1e84a87bfc60e2a07116e0a6dbb3ed44c5bbaa39aa152d2d1c43ff1b990603" %}
 
 package:
   name: {{ name }}
@@ -26,13 +26,13 @@ requirements:
   run:
     - conda-forge-pinning 2024.06.01.05.54.15
     - python 3.10.*
-    - conda 24.5.*
+    - conda 24.9.*
     - conda-libmamba-solver 24.1.*
-    - conda-build 24.5.*
-    - conda-index 0.4.*
-    - conda-package-streaming 0.9.*
+    - conda-build 24.7.*
+    - conda-index 0.5.*
+    - conda-package-streaming 0.11.*
     - mamba 1.5.*
-    - boa 0.17.*
+    #- boa 0.17.*
     - argh 0.31.*
     - colorlog 6.*
     - tqdm 4.66.*
diff --git a/recipes/bustools/build.sh b/recipes/bustools/build.sh
index 93f63cbb3280d..cbd3af5c9a2da 100644
--- a/recipes/bustools/build.sh
+++ b/recipes/bustools/build.sh
@@ -1,10 +1,21 @@
 #!/bin/bash
 set -euo pipefail
 
-export CPATH=$PREFIX/include
+export CPATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
+export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include"
 
-mkdir build
-cd build 
-cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX ..
-make 
-make install
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+ 
+cmake -S. -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
+	-DCMAKE_C_FLAGS="${CFLAGS} -O3" \
+	"${CONFIG_ARGS}"
+
+cmake --build build --target install -v
diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml
index fed8ae7701f0b..7e114c40dd6d9 100644
--- a/recipes/bustools/meta.yaml
+++ b/recipes/bustools/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.44.0" %}
+{% set version = "0.44.1" %}
 
 package:
   name: bustools
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz
-  sha256: e9a12be416d5d3940dd0ec3bfb0be3a481f2eea7d4411df1ab24c814332d99b8
+  sha256: 829d7ca129b4c4911cae35bc2b87cac5d3a7845387b9a6487765aec84108d732
 
 build:
   number: 0
@@ -27,14 +27,19 @@ test:
     - bustools sort
 
 about:
-  home: https://github.com/BUStools/bustools
-  license: BSD-2-Clause "Simplified" License
+  home: "https://github.com/BUStools/bustools"
+  license: 'BSD-2-Clause "Simplified" License'
   license_family: BSD
   license_file: LICENSE
   summary: |
     bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.
+  dev_url: "https://github.com/BUStools/bustools"
+  doc_url: "https://bustools.github.io/manual"
 
 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
+  identifiers:
+    - biotools:BUStools
+    - doi:10.1038/s41587-021-00870-2
diff --git a/recipes/centrifuge-core/build.sh b/recipes/centrifuge-core/build.sh
index 78918ac22ed5a..e589cb971645c 100644
--- a/recipes/centrifuge-core/build.sh
+++ b/recipes/centrifuge-core/build.sh
@@ -1,12 +1,24 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
 mkdir -p $PREFIX/bin
 
+case $(uname -m) in
+    aarch64 | arm64)
+        ARCH_FLAGS=(POPCNT_CAPABILITY=0 "RELEASE_FLAGS=${CXXFLAGS} -fsigned-char")
+        ;;
+    *)
+        ARCH_FLAGS=("RELEASE_FLAGS=${CXXFLAGS}")
+        ;;
+esac
+
 sed "/^GCC/d;/^CC =/d;/^CPP =/d;/^CXX =/d" < Makefile > Makefile.new
 mv Makefile.new Makefile
 cat Makefile
-make CC=$CC CXX=$CXX RELEASE_FLAGS="$CXXFLAGS"
+make -j"${CPU_COUNT}" CC=$CC CXX=$CXX "${ARCH_FLAGS[@]}"
 make install prefix=$PREFIX
 
diff --git a/recipes/centrifuge-core/meta.yaml b/recipes/centrifuge-core/meta.yaml
index 5381ccdd5d741..b9347c7e85535 100644
--- a/recipes/centrifuge-core/meta.yaml
+++ b/recipes/centrifuge-core/meta.yaml
@@ -1,19 +1,19 @@
 {% set name = "centrifuge-core" %}
-{% set version = "1.0.4.1" %}
+{% set version = "1.0.4.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("centrifuge-core", max_pin="x.x") }}
 
 source:
   url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc
+  sha256: db142790522a72971c7deda7d22e1f29fce54dbf23afc2e40def9f5a764f4c99
 
 requirements:
   build:
@@ -34,11 +34,17 @@ test:
     - centrifuge --help
 
 about:
-  home: https://github.com/DaehwanKimLab/centrifuge
-  license: GPL3
+  home: http://www.ccb.jhu.edu/software/centrifuge
+  license: GPL-3.0-only
+  license_file: LICENSE
+  license_family: GPL3
   summary: 'Classifier for metagenomic sequences. Does not include evaluation scripts'
+  dev_url: https://github.com/DaehwanKimLab/centrifuge
+  doc_url: https://genome.cshlp.org/content/26/12/1721
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:Centrifuge
     - doi:10.1101/gr.210641.116
diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml
index fce1fe935652b..e2475be1dea44 100644
--- a/recipes/centrifuge/meta.yaml
+++ b/recipes/centrifuge/meta.yaml
@@ -1,19 +1,19 @@
 {% set name = "centrifuge" %}
-{% set version = "1.0.4.1" %}
+{% set version = "1.0.4.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("centrifuge", max_pin="x.x") }}
 
 source:
   url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc
+  sha256: db142790522a72971c7deda7d22e1f29fce54dbf23afc2e40def9f5a764f4c99
   patches:
     - centrifuge-linux-aarch64.patch # [linux and aarch64]
 
diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml
index 7902d97a06e40..87a5b05a258f1 100644
--- a/recipes/clinvar-this/meta.yaml
+++ b/recipes/clinvar-this/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.18.2" %}
-{% set sha256 = "b3064769e3cf62bd19d12523d391496bce96ce2c057df2b49e53f922ef1369fb" %}
+{% set version = "0.18.3" %}
+{% set sha256 = "e7412c87b064d11998708dde1e17bf85ce0622802b3dbb48c66176da304a5120" %}
 
 package:
   name: clinvar-this
@@ -10,36 +10,46 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   noarch: python
   run_exports:
     - {{ pin_subpackage("clinvar-this", max_pin="x.x") }}
   number: 0
+  entry_points:
+    - clinvar-this=clinvar_this.cli:cli
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.6
     - pip
+    - setuptools
   run:
-    - python >=3.8
+    - python >=3.6
     - pysam >=0.10.0
     - logzero
-    - requests
-    - attrs
-    - cattrs
+    - httpx >=0.24
+    - pydantic >=2.5
     - python-dateutil
     - click
     - toml
     - tabulate
     - jsonschema
+    - xmltodict >=0.13.0,<0.15
+    - tqdm >=4.0
+    - protobuf >=3.20.2,<6.0
 
 test:
   imports:
     - clinvar_this
     - clinvar_api
+    - clinvar_data
+  commands:
+    - clinvar-this --help
 
 about:
   home: https://github.com/bihealth/clinvar-this
   license: MIT
   license_family: MIT
-  summary: ClinVar Submission API Made Easy
+  license_file: LICENSE
+  summary: "ClinVar Submission API Made Easy."
+  dev_url: https://github.com/bihealth/clinvar-this
diff --git a/recipes/cloudspades/0001-change-verbosity-remove-expr.patch b/recipes/cloudspades/0001-change-verbosity-remove-expr.patch
new file mode 100644
index 0000000000000..56ba08ed62cc7
--- /dev/null
+++ b/recipes/cloudspades/0001-change-verbosity-remove-expr.patch
@@ -0,0 +1,43 @@
+diff -Naur a/assembler/spades_compile.sh b/assembler/spades_compile.sh
+--- a/assembler/spades_compile.sh	2024-05-26 14:36:40
++++ b/assembler/spades_compile.sh	2024-05-27 13:00:03
+@@ -37,10 +37,10 @@ check_whether_OPTARG_is_an_integer() {
+ }
+ 
+ # return the argument first character
+-str_head() { echo "$(expr substr "$1" 1 1)"; }
++str_head() { echo "${1::1}"; }
+ 
+ # return the argument without the first character
+-str_tail() { echo "$(expr substr "$1" 2 $((${#1}-1)))"; }
++str_tail() { echo "${1:1}"; }
+ 
+ print_help() {
+   echo
+@@ -221,11 +221,21 @@ else
+   ADDITIONAL_FLAGS="$ADDITIONAL_FLAGS -DSPADES_BUILD_INTERNAL=OFF"
+ fi
+ 
+-cd "$WORK_DIR"
+-cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $ADDITIONAL_FLAGS "$BASEDIR/src"
+-make -j $AMOUNT_OF_THREADS
+-make install
+-cd "$PREFIX"
++if [[ `uname` == "Darwin" ]]; then
++        export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
++       export CFLAGS="${CFLAGS} -Wunused-command-line-argument"
++       export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
++else
++        export CONFIG_ARGS=""
++fi
++
++cd "${WORK_DIR}"
++cmake -S "${BASEDIR}/src" -B . -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
++       -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
++       -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
++       -DCMAKE_C_FLAGS="${CFLAGS}" "${ADDITIONAL_FLAGS}" \
++       "${CONFIG_ARGS}"
++cmake --build . --target install -j "${AMOUNT_OF_THREADS}" -v
+ 
+ if [ $RUN_TESTS = "y" ]; then
+   cd "$BASEDIR"
diff --git a/recipes/cloudspades/build.sh b/recipes/cloudspades/build.sh
new file mode 100644
index 0000000000000..db97bf699cf4f
--- /dev/null
+++ b/recipes/cloudspades/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -e -o pipefail -x
+
+#export LIBRARY_PATH="${PREFIX}/lib"
+#export INCLUDE_PATH="${PREFIX}/include"
+#export CFLAGS="${CFLAGS} -O3 -fcommon"
+#export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY"
+
+case $(uname) in
+	Linux)
+		THREADS="-rj${CPU_COUNT}"
+		;;
+	Darwin)
+		THREADS=""
+		;;
+esac
+
+mkdir -p ${PREFIX}/bin ${PREFIX}/share
+cd assembler
+./spades_compile.sh "${THREADS}"
diff --git a/recipes/cloudspades/meta.yaml b/recipes/cloudspades/meta.yaml
new file mode 100644
index 0000000000000..86a36f47254c5
--- /dev/null
+++ b/recipes/cloudspades/meta.yaml
@@ -0,0 +1,54 @@
+{% set name = "cloudspades" %}
+{% set version = "3.16.0" %}
+{% set sha256 = "5972a76722fadf9527675fea3884a03ca864b153b8de9dd94532b1b797de04aa" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 2
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('cloudspades', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - make
+    - pkg-config
+  host:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - zlib
+    - bzip2
+  run:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - python >=3.8
+
+test:
+  commands:
+    - spades.py --version 2>&1 | grep {{ version }}
+    - metaspades.py --version 2>&1 | grep {{ version }}
+    - spades-kmercount -h 2>&1 | grep spades-kmercount
+    - spades-gmapper 2>&1 | grep spades-gmapper
+    - spades-gbuilder 2>&1 | grep spades-gbuilder
+
+about:
+  home: "https://github.com/ablab/spades"
+  license: "GPL-2.0-only"
+  license_family: GPL
+  license_file: 'assembler/LICENSE'
+  summary: "A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging)."
+  dev_url: "https://github.com/ablab/spades/tree/cloudspades-0.1"
+  doc_url: "https://github.com/ablab/spades/tree/cloudspades-ismb"
+
+extra:
+  recipe-maintainers:
+    - pdimens
diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml
index dd607eeb31f7e..61859cdf5086d 100644
--- a/recipes/cmat/meta.yaml
+++ b/recipes/cmat/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cmat" %}
-{% set version = "3.3.0" %}
+{% set version = "3.3.1" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz
-  sha256: d39137937c2827b401fe7ca10ccaaf4f8dbbac049e7ea5b86ded6713bf1efdba
+  sha256: 2cce0cd4775242590ffb557e9b1969d3bcf6c1f92b3ba9be8d086ac11ad0e56f
 
 build:
   number: 0
diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml
index 9e74412a866f8..4d4729025442b 100644
--- a/recipes/cogent3/meta.yaml
+++ b/recipes/cogent3/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cogent3" %}
-{% set version = "2024.7.19a6" %}
+{% set version = "2024.7.19a8" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: dae78c99be59e4a2283cd1e60ea1e35029132296c1b2c4fc750a5f28f809a72b
+  sha256: 7d046813b004c09de379b6d001b48ff93c0193923cc5b809efb5cfa25fb278c7
 
 build:
   noarch: python
diff --git a/recipes/cosigt/meta.yaml b/recipes/cosigt/meta.yaml
index f4698f2f97ca0..5b52ccd1d98e6 100644
--- a/recipes/cosigt/meta.yaml
+++ b/recipes/cosigt/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cosigt" %}
-{% set version = "0.1.2" %}
+{% set version = "0.1.3" %}
 
 package:
   name: {{ name }}
@@ -11,8 +11,8 @@ build:
       - {{ pin_subpackage(name, max_pin='x.x') }}
 
 source:
-  - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/v{{ version }}.tar.gz
-    sha256: 8cd92c395643720492cc1626d16aa5258bf44a6f448c2ea3407a257bf0ab6416
+  - url: https://github.com/davidebolo1993/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+    sha256: 3a4efa472188c4820bb6d0c56225d9d6c7bb2120cdfb40b4c31892b36ec78652
 
 requirements:
   build:
diff --git a/recipes/d4binding/build.sh b/recipes/d4binding/build.sh
index 564717ff7b0ef..463bbbe302d53 100644
--- a/recipes/d4binding/build.sh
+++ b/recipes/d4binding/build.sh
@@ -5,8 +5,10 @@ set -x
 # TODO: Remove the following export when pinning is updated and we use
 #       {{ compiler('rust') }} in the recipe.
 export \
-    CARGO_NET_GIT_FETCH_WITH_CLI=true \
-    CARGO_HOME="${BUILD_PREFIX}/.cargo"
+	CARGO_NET_GIT_FETCH_WITH_CLI=true \
+	CARGO_HOME="${BUILD_PREFIX}/.cargo"
+
+cp $RECIPE_DIR/build_htslib.sh d4-hts/build_htslib.sh
 
 cd d4binding 
 ./install.sh
diff --git a/recipes/d4binding/build_htslib.sh b/recipes/d4binding/build_htslib.sh
new file mode 100644
index 0000000000000..e3a214a0d2ec0
--- /dev/null
+++ b/recipes/d4binding/build_htslib.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+if [ "${DOCS_RS}" = "1" ]
+then
+	exit 0
+fi
+
+set -ex
+
+pushd ${OUT_DIR}
+
+HTSLIB_VERSION=${1}
+
+rm -rf ${OUT_DIR}/htslib
+
+git clone -b ${HTSLIB_VERSION} http://github.com/samtools/htslib.git
+
+cd htslib
+
+cat > config.h << CONFIG_H
+#define HAVE_LIBBZ2 1
+#define HAVE_DRAND48 1
+CONFIG_H
+
+perl -i -pe 's/hfile_libcurl\.o//g' Makefile
+	
+function is_musl() {
+	if [ ! -z $(echo $TARGET | grep musl) ]; then 
+		return 0
+	else
+		return 1
+	fi
+}
+
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+
+
+if [ "x${ZLIB_SRC}" != "x" ]
+then
+	tar xz ${ZLIB_SRC}
+else
+	curl -L 'http://github.com/madler/zlib/archive/refs/tags/v1.2.11.tar.gz' | tar xz
+fi
+cd zlib-1.2.11
+is_musl && CC=musl-gcc ./configure || ./configure
+make libz.a
+cp libz.a ..
+cd ..
+
+#The original file in the repo is lacking -L in the curl command so it doen't work
+curl -L http://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz | tar xz
+cd bzip2-1.0.8
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+is_musl || perl -i -pe 's/CFLAGS=/CFLAGS=-fPIC /g' Makefile
+make
+cp libbz2.a ..
+cd ..
+
+perl -i -pe 's/CPPFLAGS =/CPPFLAGS = -Izlib-1.2.11 -Ibzip2-1.0.8/g' Makefile
+
+is_musl || perl -i -pe 's/CFLAGS *=/CFLAGS = -fPIC/g' Makefile
+
+make -j8 lib-static
\ No newline at end of file
diff --git a/recipes/d4binding/meta.yaml b/recipes/d4binding/meta.yaml
index cbbb959e092d6..a5507dd7ca35d 100644
--- a/recipes/d4binding/meta.yaml
+++ b/recipes/d4binding/meta.yaml
@@ -1,29 +1,32 @@
-{% set version = "0.3.4" %}
+{% set name = "d4binding" %}
+{% set version = "0.3.11" %}
 
 package:
-  name: d4binding
+  name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("d4binding", max_pin="x.x") }}
 
 source:
-  # TODO: use formal release number when 0.3.5 is released
-  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}-3.tar.gz
-  sha256: 05e1a410b77c34d7d188e69ef607eaa9f0babcc9817c558362203fc3f1f2219c
+  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - rust >=1.30
-    - gcc #[not osx]
+    - gcc  # [not osx]
     - clangdev
     - pkg-config
     - make
     - cmake
   run:
     - starcode
+
 test:
   commands:
     - "true"
@@ -31,8 +34,11 @@ test:
 about:
   home: https://github.com/38/d4-format
   license: MIT
+  license_family: MIT
   summary: |
-    The C/C++ binding for the D4 file format
+    The C/C++ binding for the D4 file format.
+  dev_url: https://github.com/38/d4-format
+
 extra:
   recipe-maintainers:
     - haohou
diff --git a/recipes/d4tools/meta.yaml b/recipes/d4tools/meta.yaml
index 185f9b3671124..17f8a4c9838dc 100644
--- a/recipes/d4tools/meta.yaml
+++ b/recipes/d4tools/meta.yaml
@@ -1,7 +1,8 @@
+{% set name = "d4tools" %}
 {% set version = "0.3.11" %}
 
 package:
-  name: d4tools
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -9,7 +10,7 @@ source:
   sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('d4tools', max_pin="x.x") }}
 
@@ -35,7 +36,7 @@ about:
   license: MIT
   license_family: MIT
   summary: |
-    The D4 command line utility program
+    The D4 command line utility program.
   dev_url: https://github.com/38/d4-format
 
 extra:
diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh
index 17d5db214e9a0..e3d6bbba51363 100644
--- a/recipes/devider/build.sh
+++ b/recipes/devider/build.sh
@@ -1,10 +1,21 @@
-#!/bin/bash -euo
+#!/bin/bash
+
+set -xeuo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
 # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+export CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
 cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
-RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+
+case $(uname -m) in
+    aarch64 | arm64)
+        FEATURES="--features neon --no-default-features"
+        ;;
+    *)
+        FEATURES=""
+        ;;
+esac
+
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . ${FEATURES}
 cp scripts/* $PREFIX/bin
diff --git a/recipes/devider/devider-aarch64.patch b/recipes/devider/devider-aarch64.patch
new file mode 100644
index 0000000000000..6c2478c0cccfa
--- /dev/null
+++ b/recipes/devider/devider-aarch64.patch
@@ -0,0 +1,14 @@
+--- Cargo.toml.orig	2024-10-14 10:59:48.140000000 +0000
++++ Cargo.toml	2024-10-14 11:03:33.120000000 +0000
+@@ -13,9 +13,9 @@
+ rayon="1.7"
+ rand="0.8"
+ rand_core="0.6"
+-rust-htslib= { version = "0.44", default-features = false }
++rust-htslib= { version = "0.47", default-features = false }
+ clap = { version = "=4.2.0", features = ["derive"] }
+-block-aligner = { version = "0.4", default-features = false }
++block-aligner = { version = "0.5", default-features = false }
+ debruijn = "0.3"
+ simple_logger="4"
+ log="0.4"
diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml
index b9ea2b34e8c0d..90c59b5125124 100644
--- a/recipes/devider/meta.yaml
+++ b/recipes/devider/meta.yaml
@@ -7,9 +7,11 @@ package:
 source:
   url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
   sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+  patches:
+    - devider-aarch64.patch # [aarch64]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('devider', max_pin="x.x") }}
 
@@ -20,6 +22,8 @@ requirements:
     - cargo-bundle-licenses
     - make
     - cmake >=3.12
+  host:
+    - clangdev >=16,<17 # [linux and aarch64]
   run:
     - python 
     - samtools
@@ -43,5 +47,7 @@ about:
   summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - bluenote-1577
diff --git a/recipes/diamond/build.sh b/recipes/diamond/build.sh
index fb2b5daab9c6c..f1d4252c8d0ac 100644
--- a/recipes/diamond/build.sh
+++ b/recipes/diamond/build.sh
@@ -1,22 +1,23 @@
 #!/bin/bash
 
 sed -i.bak 's/-march=native/-march=x86-64/' CMakeLists.txt
+rm -rf *.bak
 
-mkdir build
-cd build
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
 
+cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
+	-DWITH_ZSTD=ON \
+	-DZSTD_LIBRARY="${PREFIX}/lib/libzstd.a" \
+	-DZSTD_INCLUDE_DIR="${PREFIX}/include" \
+	-DBLAST_LIBRARY_DIR="${PREFIX}/lib/ncbi-blast+" \
+	-DCMAKE_OSX_DEPLOYMENT_TARGET="" \
+	"${CONFIG_ARGS}"
 
-cmake .. \
-      -DCMAKE_INSTALL_PREFIX=$PREFIX \
-      -DCMAKE_PREFIX_PATH=$PREFIX \
-      -DCMAKE_LIBRARY_PATH="$PREFIX" \
-      -DWITH_ZSTD=on \
-      -DZSTD_LIBRARY=$PREFIX/lib/libzstd.a \
-      -DZSTD_INCLUDE_DIR=$PREFIX/include/ \
-      -DBLAST_LIBRARY_DIR=$PREFIX/lib/ncbi-blast+ \
-      -DCMAKE_OSX_DEPLOYMENT_TARGET=""
-
-cmake --build . --config Release --target install
-
-# Reference link:
-# https://github.com/conda/conda-recipes/blob/master/boost/build.sh
+cmake --build build --target install -v
diff --git a/recipes/diamond/meta.yaml b/recipes/diamond/meta.yaml
index d35213fa65257..355240e301805 100644
--- a/recipes/diamond/meta.yaml
+++ b/recipes/diamond/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "2.1.9" %}
-{% set sha256 = "4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88" %}
+{% set version = "2.1.10" %}
+{% set sha256 = "c6ede5df30d9d496af314e740964c35a0e358458d9c8d9b8dd517d69828d9981" %}
 
 package:
   name: diamond
@@ -10,7 +10,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage('diamond', max_pin="x") }}
 
@@ -22,25 +22,28 @@ requirements:
     - make
   host:
     - zlib
-    - blast
     - zstd-static
-  run:
-    - blast
-    - zlib
 
 test:
   commands:
     - diamond --help 2>&1 > /dev/null
 
 about:
-  home: https://github.com/bbuchfink/diamond
-  license: GPL-3.0-or-later
+  home: "https://github.com/bbuchfink/diamond"
+  license: "GPL-3.0-or-later"
   license_family: GPL3
   license_file: LICENSE
-  summary: Accelerated BLAST compatible local sequence aligner
-  doc_url: https://github.com/bbuchfink/diamond/wiki
+  summary: "Accelerated BLAST compatible local sequence aligner."
+  doc_url: "https://github.com/bbuchfink/diamond/wiki"
+  dev_url: "https://github.com/bbuchfink/diamond"
 
 extra:
   identifiers:
-    - biotools:Diamond
+    - biotools:diamond
+    - usegalaxy-eu:bg_diamond
+    - usegalaxy-eu:bg_diamond_makedb
+    - usegalaxy-eu:bg_diamond_view
     - doi:10.1038/s41592-021-01101-x
+  additional-platforms:
+    - osx-arm64
+    - linux-aarch64
diff --git a/recipes/dnmtools/build.sh b/recipes/dnmtools/build.sh
index dd8b881bae132..9f3aa85e5c860 100644
--- a/recipes/dnmtools/build.sh
+++ b/recipes/dnmtools/build.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 
-./configure --prefix=$PREFIX
-make CXXFLAGS="-O3 -DNDEBUG -D_LIBCPP_DISABLE_AVAILABILITY"
+export M4="$BUILD_PREFIX/bin/m4"
+autoreconf -if
+./configure --prefix="${PREFIX}"
+
+make CXXFLAGS="${CXXFLAGS} -O3 -DNDEBUG -D_LIBCPP_DISABLE_AVAILABILITY" -j"${CPU_COUNT}"
 make install
diff --git a/recipes/dnmtools/meta.yaml b/recipes/dnmtools/meta.yaml
index 56c7d565d5f49..d52deda3af845 100644
--- a/recipes/dnmtools/meta.yaml
+++ b/recipes/dnmtools/meta.yaml
@@ -1,48 +1,56 @@
-{% set version = "1.4.3" %}
+{% set version = "1.4.4" %}
 
 package:
   name: dnmtools
   version: {{ version }}
 
+source:
+  url: https://github.com/smithlabcode/dnmtools/releases/download/v{{ version }}/dnmtools-{{ version }}.tar.gz
+  sha256: 56fc62ef1d41cdafa30c98d6cfbcb3707a125921618a1808075eaafb29d22edf
+
 build:
   number: 0
   run_exports:
     # dnmtools is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('dnmtools', max_pin="x.x") }}
 
-source:
-  url: https://github.com/smithlabcode/dnmtools/releases/download/v{{ version }}/dnmtools-{{ version }}.tar.gz
-  sha256: 2ec96953d088cfde895d2b5afc77197850d50d7046bb6febce52a86db805ef17
-
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - autoconf
     - automake
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
+    - libtool
   host:
     - zlib
     - htslib
     - gsl
+    - llvm-openmp  # [osx]  
+    - libgomp      # [linux]
   run:
     - htslib
     - gsl
+    - llvm-openmp  # [osx]  
+    - libgomp      # [linux]
+
+test:
+  commands:   
+    - dnmtools
 
 about:
   home: https://github.com/smithlabcode/dnmtools
-  license: GPL-3.0-or-later
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
   summary: |
-    dnmtools is a set of tools for analyzing DNA methylation data from bisulfite sequencing
-  doc_url: 'https://dnmtools.readthedocs.io/'
-
-test:
-  commands:
-    - dnmtools
+    dnmtools is a set of tools for analyzing DNA methylation data from bisulfite sequencing.
+  doc_url: 'https://dnmtools.readthedocs.io'
+  dev_url: "https://github.com/smithlabcode/dnmtools"
 
 extra:
   recipe-maintainers:
     - andrewdavidsmith
     - guilhermesena1
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml
index 172199dff30e6..b26c1ef097798 100644
--- a/recipes/dxpy/meta.yaml
+++ b/recipes/dxpy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "dxpy" %}
-{% set version = "0.383.1" %}
+{% set version = "0.384.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 377af4014a5f27efd6fe9478d0fa9c30ced245947fbd2e2e5713c8a37db598b0
+  sha256: 17e29e9f58843c2639d53ea02b0dfd5c9940ad4ff20ab9e4df895a664f07e392
 
 build:
   number: 0
diff --git a/recipes/easypqp/meta.yaml b/recipes/easypqp/meta.yaml
index d4de88853b783..5157353791118 100644
--- a/recipes/easypqp/meta.yaml
+++ b/recipes/easypqp/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "easypqp" %}
-{% set version = "0.1.49" %}
-{% set sha256 = "96fffd59e617de0007f1fbe88ab223d605a7d4a4e94a7b4f4d4a94b4016e327c" %}
+{% set version = "0.1.50" %}
+{% set sha256 = "d3ebc1c7cbe61f081c5ab71e76e7130aa7fae955895ffe8f719363b29870a000" %}
 
 package:
   name: {{ name|lower }}
@@ -23,6 +23,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - numba
diff --git a/recipes/el_gato/build.sh b/recipes/el_gato/build.sh
deleted file mode 100644
index 73991f59b0666..0000000000000
--- a/recipes/el_gato/build.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-$PYTHON -m pip install . -vv
-
-mkdir -p $PREFIX/bin/db
-cp el_gato/db/* $PREFIX/bin/db/
diff --git a/recipes/el_gato/meta.yaml b/recipes/el_gato/meta.yaml
index 0c15f3b4c1530..0e7fe03025f68 100644
--- a/recipes/el_gato/meta.yaml
+++ b/recipes/el_gato/meta.yaml
@@ -1,10 +1,10 @@
 {% set name = "el_gato" %}
-{% set version = "1.19.0" %}
-{% set hash = "ad390572ce785707b67a00f25978c4032981ac7e6149ddc423443e9189b30e75" %}
+{% set version = "1.20.1" %}
+{% set hash = "3c19594caa7aff4d1fee7a844f645c640b08adbb9fc9926439ab2c2891c88de9" %}
 {% set user = "appliedbinf" %}
 
 package:
-  name: el_gato
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -14,14 +14,19 @@ source:
 build:
   number: 0
   noarch: generic
+  script:
+    - mkdir -p $PREFIX/bin/db
+    - cp -rf el_gato/db/* $PREFIX/bin/db/
+    - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
+    - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
+  build:
+    - python
   host:
     - python >=3.8,<3.12
     - pip
-    - setuptools
   run:
     - python >=3.8,<3.12
     - minimap2 >=2.24
@@ -31,13 +36,22 @@ requirements:
     - nextflow
     - fpdf2
     - packaging
+    - colorama  # [linux]
+    - importlib-metadata  # [py <= 38]
+
+extra:
+  skip-lints:
+    - should_be_noarch_python # database files aren't found properly when built with noarch: python
 
 test:
   commands:
     - el_gato.py --version
 
 about:
-  home: https://github.com/{{ user }}/{{ name }}
+  home: "https://github.com/{{ user }}/{{ name }}"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: Perform Legionella pneumophila Sequence Based Typing (SBT) from short reads or assemblies
+  summary: "Perform Legionella pneumophila Sequence Based Typing (SBT) from short reads or assemblies."
+  dev_url: "https://github.com/{{ user }}/{{ name }}"
+  doc_url: "https://github.com/appliedbinf/el_gato/blob/{{ version }}/README.md"
diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml
index 4bb5ccbc704d1..5592412e043df 100644
--- a/recipes/ensembl-vep/meta.yaml
+++ b/recipes/ensembl-vep/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ensembl-vep" %}
-{% set version = "112.0" %}
+{% set version = "113.0" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz
-  sha256: aaa1dc9815f41fec4efd466fcb6607bdfcd407b4f1b07b412412e93cc1bd0f40
+  sha256: 5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164
 
 build:
   number: 0
diff --git a/recipes/ezcharts/meta.yaml b/recipes/ezcharts/meta.yaml
index d439af6dc504d..35cd0dcea4e79 100644
--- a/recipes/ezcharts/meta.yaml
+++ b/recipes/ezcharts/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ezcharts" %}
-{% set version = "0.10.2" %}
+{% set version = "0.11.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/ezcharts-{{ version }}.tar.gz
-  sha256: 5357d3104057a14cb05afda3ef252771fcc00ced3200bd25a0195795ed6daae1
+  sha256: d643951b43812f23e2079294446636d1574e5f78d027d3679a2ab9ff391deb07
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - python >=3.7
     - bokeh >=3.1.0,<3.2.dev0
@@ -34,9 +35,9 @@ requirements:
     - scipy
     - seaborn-base >=0.12.0,<0.13.dev0
     - sigfig
-    - natsort
+    - natsort ==8.4.0
     - pysam
-    - pymsaviz
+    - pymsaviz ==0.4.2
     - biopython
 
 test:
diff --git a/recipes/fastplong/build.sh b/recipes/fastplong/build.sh
new file mode 100644
index 0000000000000..a7f3dbddf899c
--- /dev/null
+++ b/recipes/fastplong/build.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+set -xeu -o pipefail
+mkdir -p $PREFIX/bin
+
+make -j ${CPU_COUNT} INCLUDE_DIRS="$PREFIX/include" LIBRARY_DIRS="$PREFIX/lib"
+make install
diff --git a/recipes/fastplong/meta.yaml b/recipes/fastplong/meta.yaml
new file mode 100644
index 0000000000000..69fdcd2e451d7
--- /dev/null
+++ b/recipes/fastplong/meta.yaml
@@ -0,0 +1,42 @@
+{% set version="0.2.0" %}
+
+package:
+  name: fastplong
+  version: {{ version }}
+
+source:
+  url: https://github.com/OpenGene/fastplong/archive/v{{ version }}.tar.gz
+  sha256: 563970cb2c89c8092e4a2ce4f3e5ac73e039a9aa025845defd9d93c8cf6b0303
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("fastplong", max_pin="x.x") }}
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - isa-l
+    - libdeflate
+  run:
+    - isa-l
+    - libdeflate
+
+test:
+  commands:
+    - fastplong --help
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+
+about:
+  home: https://github.com/OpenGene/fastplong
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Ultra-fast preprocessing and quality control for long-read sequencing data
diff --git a/recipes/fastq-dl/meta.yaml b/recipes/fastq-dl/meta.yaml
index 0f276e73c516e..892a52d2045f2 100644
--- a/recipes/fastq-dl/meta.yaml
+++ b/recipes/fastq-dl/meta.yaml
@@ -1,30 +1,32 @@
-{% set version = "2.0.4" %}
+{% set name = "fastq-dl" %}
+{% set version = "3.0.0" %}
 
 package:
-  name: fastq-dl
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/f/fastq_dl/fastq_dl-{{ version }}.tar.gz
-  sha256: 201a75f7e7b08d1eb56c625c98f92ad39e9e683e1921bb60a24a38a158a2daa8
+  sha256: de85e3fcc60c2f2fb9313336df9706add440b0f89963f28a46fa75e5ff041a0a
 
 build:
   number: 0
   noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
   entry_points:
-    - fastq-dl = fastq_dl.fastq_dl:main
-  script: "{{ PYTHON }} -m pip install . -vv"
+    - fastq-dl = fastq_dl.cli.download:main
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   host:
-    - python >=3.7
-    - poetry =1.3
+    - python >=3.9
+    - poetry-core
     - pip
-
   run:
     - executor
     - pigz
-    - python >=3.7
+    - python >=3.9
     - pysradb >=1.4
     - requests
     - rich-click >=1.6.0
@@ -43,3 +45,7 @@ about:
   license: MIT
   license_file: LICENSE
   summary: A tool to download FASTQs associated with Study, Experiment, or Run accessions.
+
+extra:
+  recipe-maintainers:
+    - rpetit3
diff --git a/recipes/flexi-formatter/meta.yaml b/recipes/flexi-formatter/meta.yaml
index 497fd0006fc48..cedccccffea85 100644
--- a/recipes/flexi-formatter/meta.yaml
+++ b/recipes/flexi-formatter/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "flexi-formatter" %}
-{% set version = "0.0.2" %}
+{% set version = "1.0.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flexi_formatter-{{ version }}.tar.gz
-  sha256: c3a054fe1b8a3f9ccb307559ef125236d3f6f134dd35be4f3862e8b136ebd8bd
+  sha256: 77e24d0619d287f49e2aaf0daa14f934b20b1d5a52a5d4a427738bd21ec38b84
 
 build:
   entry_points:
diff --git a/recipes/fmsi/0001-Makefile.patch b/recipes/fmsi/0001-Makefile.patch
new file mode 100644
index 0000000000000..517f6b2a3cc19
--- /dev/null
+++ b/recipes/fmsi/0001-Makefile.patch
@@ -0,0 +1,29 @@
+diff --git a/src/Makefile b/src/Makefile
+index 6272ad5..473407a 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,10 +1,10 @@
+ .PHONY: all clean 
+-CXX=									g++
+-CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O2
+-PROG=									../fmsi
+-INCLUDES-PATH?=.
++CXX=									${CXX}
++CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O3
++PROG=									${PREFIX}/bin/fmsi
++INCLUDES-PATH?=							${PREFIX}
+ INCLUDES=							-I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib 
+-LIBS=									-lz -lsdsl -ldivsufsort -ldivsufsort64
++LIBS+=									-lz -lsdsl -ldivsufsort -ldivsufsort64 -L${PREFIX}/lib
+ 
+ all:$(PROG)
+ 
+@@ -14,7 +14,7 @@ include/sdsl/suffix_arrays.hpp: sdsl-lite/build/Makefile
+ 	$(MAKE) -C sdsl-lite/build install
+ 
+ sdsl-lite/build/Makefile:
+-	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../.. ..
++	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+ 
+ 
+ $(PROG): $(wildcard *.cpp *.c *.h) ./include/sdsl/suffix_arrays.hpp version.h
diff --git a/recipes/fmsi/build.sh b/recipes/fmsi/build.sh
new file mode 100644
index 0000000000000..aa6c47f645057
--- /dev/null
+++ b/recipes/fmsi/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+	export CXXFLAGS="${CXXFLAGS}"
+fi
+
+make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
+	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \
+	-j"${CPU_COUNT}"
+
+chmod 0755 ${PREFIX}/bin/fmsi
diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml
new file mode 100644
index 0000000000000..5db343b3713d3
--- /dev/null
+++ b/recipes/fmsi/meta.yaml
@@ -0,0 +1,48 @@
+{% set version = "0.3.0" %}
+{% set sha256 = "441d9f5808c7568ae237b5bb45db9328185fee43628eb0a4407ae7da0bdcf3bc" %}
+
+package:
+  name: fmsi
+  version: {{ version }}
+
+source:
+  url: https://github.com/OndrejSladky/fmsi/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    - 0001-Makefile.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('fmsi', max_pin="x.x") }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - sdsl-lite
+  run:
+    - sdsl-lite
+
+test:
+  commands:
+    - fmsi -h 2>&1 | grep "FMSI"
+
+about:
+  home: "https://github.com/OndrejSladky/fmsi"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform."
+  dev_url: "https://github.com/OndrejSladky/fmsi"
+  doc_url: "https://github.com/OndrejSladky/fmsi/blob/v{{ version }}/README.md"
+
+extra:
+  identifiers:
+    - doi:10.1101/2024.03.06.583483
+    - doi:10.1101/2023.02.01.526717
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/gempipe/meta.yaml b/recipes/gempipe/meta.yaml
index 942b8f4e376b1..986fcbbf46404 100755
--- a/recipes/gempipe/meta.yaml
+++ b/recipes/gempipe/meta.yaml
@@ -1,20 +1,19 @@
-{% set version = "1.35.4" %}
+{% set name = "gempipe" %}
+{% set version = "1.37.0" %}
 
 package:
-    name: "gempipe"
+    name: {{ name }}
     version: {{ version }}
 
-
 source:
-    url: https://github.com/lazzarigioele/gempipe/archive/v{{ version }}.tar.gz
-    sha256: 10bb83284848f8c21baa4069150e65e5a092771b5c5b6396d1e58c33431960a1
-
+    url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/gempipe-{{ version }}.tar.gz
+    sha256: 76b9f005394ee36b7e886fc6417ead37a378563a65c80f653b1c31ea816bbd4a
 
 build:
     number: 0  
     noarch: python
     script: 
-        - {{ PYTHON }} -m pip install . -vv --no-deps  
+        - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
     entry_points:
         - gempipe = gempipe:main
     run_exports:
@@ -25,9 +24,7 @@ requirements:
     host:
         - python >=3.9
         - pip
-        - poetry >=1.7.1
-        - poetry-core >=1.8.1
-        - ipython >=8.7.0
+        - poetry-core >=1.0.0
     run:
         - python >=3.9
         - ipython >=8.7.0
@@ -46,9 +43,9 @@ requirements:
         - diamond >=2.0.15
         - eggnog-mapper >=2.1.7
         - matplotlib-base >=3.7.0
-        - seaborn >=0.13.0
-        
-
+        - seaborn-base >=0.13.0
+        - scipy >=1.10.0
+        - scikit-learn >=1.3.0
 
 test:
     imports:
@@ -59,17 +56,15 @@ test:
         - gempipe derive --help
         - gempipe autopilot --help
 
-
 about:
     home: "https://github.com/lazzarigioele/gempipe"
     summary: 'gempipe is a tool for the reconstruction of strain-specific genome-scale metabolic models.'
     license: GPL-3.0-only
+    license_family: GPL3
     license_file: LICENSE.txt
-    doc_url: "https://gempipe.readthedocs.io/"
+    doc_url: "https://gempipe.readthedocs.io"
     dev_url: "https://github.com/lazzarigioele/gempipe"
 
-
 extra:
     recipe-maintainers:
         - lazzarigioele
-        
diff --git a/recipes/genbank/meta.yaml b/recipes/genbank/meta.yaml
index cf70bd241712c..2f7c8af7c4caf 100644
--- a/recipes/genbank/meta.yaml
+++ b/recipes/genbank/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "genbank" %}
-{% set version = "0.110" %}
+{% set version = "0.118" %}
 
 package:
   name: {{ name|lower }}
@@ -7,11 +7,10 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/genbank-{{ version }}.tar.gz
-  sha256: f9a6ba243d62934e9e5ed283d8b475ab3dd9a3760ba329a054d5f6df54a8ec45
+  sha256: f37d0d1ca680bda68d03385cc0ce966b9023cbf54a1c9a71213b730013882a5f
 
 build:
   number: 1
-  skip: True  # [py < 36]
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation
   run_exports:
     - {{ pin_subpackage('genbank', max_pin="x.x") }}
@@ -35,3 +34,8 @@ about:
   license: GPL-3.0-or-later
   license_family: GPL3
   license_file: LICENSE
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml
index 3e73bdf53321c..113e485ce3f40 100644
--- a/recipes/gencove/meta.yaml
+++ b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.21.0" %}
-{% set sha256 = "805be8b0c0f3e8d189bca16a805649e9594d455c0fa183ecd856ee3208287258" %}
+{% set version = "2.23.0" %}
+{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/gene-trajectory-python/LICENSE b/recipes/gene-trajectory-python/LICENSE
new file mode 100644
index 0000000000000..bfa86556228dd
--- /dev/null
+++ b/recipes/gene-trajectory-python/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 PCMGF-Limited
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/recipes/gene-trajectory-python/meta.yaml b/recipes/gene-trajectory-python/meta.yaml
new file mode 100644
index 0000000000000..33d13f239c17c
--- /dev/null
+++ b/recipes/gene-trajectory-python/meta.yaml
@@ -0,0 +1,62 @@
+{% set name = "gene-trajectory-python" %}
+{% set version = "1.0.4" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/gene-trajectory/gene_trajectory-{{ version }}.tar.gz
+  sha256: 133e22dd167cbc83b8d4ecffa98bfc623f98584b91d2ecf31b915aeb11072b73
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.9,<4.0a0
+    - flit-core >=3.2,<4
+    - pip
+  run:
+    - python >=3.9
+    - python-igraph >=0.10
+    - matplotlib-base >=3.6
+    - numpy >=1.25
+    - pandas >=1.5
+    - pot >=0.8.2
+    - scanpy >=1.9.3
+    - scikit-misc >=0.1.3
+    - scikit-learn >=0.24
+    - scipy >=1.8
+    - seaborn >=0.13
+    - tqdm >=4.64.1
+
+test:
+  imports:
+    - gene_trajectory
+  commands:
+    - pip check
+    - python -c "import gene_trajectory"
+  requires:
+    - pip
+
+about:
+  home: https://github.com/KlugerLab/GeneTrajectory-python
+  summary: Compute gene trajectories
+  description: |
+    Gene Trajectory is a Python package that computes and analyzes gene trajectories in single-cell data.
+    It provides tools for trajectory inference, gene expression analysis along trajectories, and visualization of results.
+
+  license: MIT
+  license_file: LICENSE
+  doc_url: https://github.com/KlugerLab/GeneTrajectory-python
+  dev_url: https://github.com/KlugerLab/GeneTrajectory-python
+
+
+extra:
+  recipe-maintainers:
+    - fra-pcmgf
diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml
index 4bf3f662ad0da..1179d9f7a73bf 100644
--- a/recipes/genmod/meta.yaml
+++ b/recipes/genmod/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "genmod" %}
-{% set version = "3.8.3" %}
+{% set version = "3.9" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 97a411f3f014557cf57aed9cc18e55e097ab7c54b191eb7995c10dd97d4bdeaf
+  sha256: bbe7ad87971b50f4165142481147738882be96e1200d10dcea79a31d614e0cf2
 
 build:
   number: 0
diff --git a/recipes/genodsp/build.sh b/recipes/genodsp/build.sh
new file mode 100644
index 0000000000000..8b3a89f8a7287
--- /dev/null
+++ b/recipes/genodsp/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash -e
+set -uex
+
+mkdir -vp "${PREFIX}/bin"
+
+make VERBOSE=1 -j ${CPU_COUNT}
+
+if ! install -v "$SRC_DIR/genodsp" "$PREFIX/bin/genodsp"; then
+    echo "Failed to install genodsp binary" >&2
+    exit 1
+fi
diff --git a/recipes/genodsp/meta.yaml b/recipes/genodsp/meta.yaml
new file mode 100644
index 0000000000000..74b6df8825a5f
--- /dev/null
+++ b/recipes/genodsp/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "genodsp" %}
+{% set version = "0.0.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rsharris/genodsp/archive/refs/tags/v{{ version }}+.zip
+  sha256: a7fb2218311d1ae5231041863d28adb8b5fffe724fc5ff2422310ce90a9f894a
+  patches:
+    - stringop-truncation.patch
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - make
+
+build:
+  number: 1
+  skip: True  # [not linux]
+  run_exports:
+    - {{ pin_subpackage('genodsp', max_pin="x.x") }}
+
+test:
+  commands:
+    - genodsp --help
+    - ls -l ${PREFIX}/bin/
+    - ${PREFIX}/bin/genodsp --help 
+
+about:
+  home: https://github.com/rsharris/genodsp
+  summary: General workbench for processing signals along genomic (chromosomal) intervals
+  license: GPL-3.0-only
+  license_file: LICENSE
+  license_url: https://github.com/rsharris/genodsp/blob/master/LICENSE
+
+extra:
+  additional-platforms:
+    - linux-aarch64
\ No newline at end of file
diff --git a/recipes/genodsp/stringop-truncation.patch b/recipes/genodsp/stringop-truncation.patch
new file mode 100644
index 0000000000000..e2699e188a854
--- /dev/null
+++ b/recipes/genodsp/stringop-truncation.patch
@@ -0,0 +1,185 @@
+diff --git a/Makefile b/Makefile
+index cf07368..d1dfb95 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,4 @@
+ CFLAGS = -O3 -Wall -Wextra -Werror
+-CC     = gcc
+ LDLIBS = -lm
+ 
+ operators = sum clump percentile add multiply mask logical minmax morphology map opio variables
+diff --git a/add.c b/add.c
+index 752dd5d..8fa4bad 100644
+--- a/add.c
++++ b/add.c
+@@ -240,7 +240,7 @@ void op_add_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+@@ -533,7 +533,7 @@ void op_subtract_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+diff --git a/genodsp.c b/genodsp.c
+index ac1704e..dffd622 100644
+--- a/genodsp.c
++++ b/genodsp.c
+@@ -1229,7 +1229,7 @@ void read_intervals
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+diff --git a/logical.c b/logical.c
+index fb295e3..45e1c20 100644
+--- a/logical.c
++++ b/logical.c
+@@ -497,7 +497,7 @@ void op_or_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+@@ -810,7 +810,7 @@ void op_and_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/mask.c b/mask.c
+index 4fd5ebd..ddd068e 100644
+--- a/mask.c
++++ b/mask.c
+@@ -253,7 +253,7 @@ void op_mask_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+@@ -548,7 +548,7 @@ void op_mask_not_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/minmax.c b/minmax.c
+index c222bd0..eae69ab 100644
+--- a/minmax.c
++++ b/minmax.c
+@@ -261,7 +261,7 @@ void op_min_in_interval_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -664,7 +664,7 @@ void op_max_in_interval_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -1941,7 +1941,7 @@ void op_min_with_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+@@ -2227,7 +2227,7 @@ void op_max_with_apply
+ 			v = NULL;
+ 			chromSpec = find_chromosome_spec (chrom);
+ 			if (chromSpec != NULL) v = chromSpec->valVector;
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		if (chromSpec == NULL) continue;
+diff --git a/multiply.c b/multiply.c
+index 4c1b550..d04cc41 100644
+--- a/multiply.c
++++ b/multiply.c
+@@ -260,7 +260,7 @@ void op_multiply_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+@@ -654,7 +654,7 @@ void op_divide_apply
+ 				if (chromSpec->flag) goto chrom_not_together;
+ 				}
+ 
+-			strncpy (prevChrom, chrom, sizeof(prevChrom));
++			safe_strncpy (prevChrom, chrom, sizeof(prevChrom));
+ 			}
+ 
+ 		// if the current chromosome is not of any interest, ignore this
+diff --git a/utilities.c b/utilities.c
+index 03d2ff1..3157538 100644
+--- a/utilities.c
++++ b/utilities.c
+@@ -493,3 +493,16 @@ char* ucommatize
+ 	return s;
+ 	}
+ 
++//
++void safe_strncpy
++   (char *dest, const char *src, size_t n)
++    {
++    #pragma GCC diagnostic push
++    #pragma GCC diagnostic ignored "-Wstringop-truncation"
++    strncpy(dest, src, n);
++    #pragma GCC diagnostic pop
++    if (n > 0)
++        {
++        dest[n-1] = '\0';  // Ensure null-termination
++        }
++    }
+diff --git a/utilities.h b/utilities.h
+index ac9cef7..87cfc2d 100644
+--- a/utilities.h
++++ b/utilities.h
+@@ -31,6 +31,8 @@ char*  skip_whitespace        (char* s);
+ char*  skip_darkspace         (char* s);
+ char*  duration_to_string     (float seconds);
+ char*  ucommatize             (const u32 v);
++void   safe_strncpy           (char *dest, const char *src, size_t n);
++
+ 
+ // miscellany
+ 
diff --git a/recipes/gw/build.sh b/recipes/gw/build.sh
index 41ea8b9fe293b..04532b916b152 100644
--- a/recipes/gw/build.sh
+++ b/recipes/gw/build.sh
@@ -2,11 +2,14 @@
 set -e
 
 # Get pre-compiled skia from jetbrains
-USE_GL=1 make prep > /dev/null 2>&1 
+USE_GL=1 make prep 2> /dev/null
 
 if [[ "$OSTYPE" != "darwin"* ]]; then
-  sed -i 's/-lEGL -lGLESv2/-lEGL -lGLESv2 -lGL -lGLX/' Makefile
-  sed -i 's/GLFW_EGL_CONTEXT_API/GLFW_NATIVE_CONTEXT_API/' src/plot_manager.cpp
+  sed -i.bak 's/-lEGL -lGLESv2/-lEGL -lGLESv2 -lGL -lGLX/' Makefile
+  sed -i.bak 's/GLFW_EGL_CONTEXT_API/GLFW_NATIVE_CONTEXT_API/' src/plot_manager.cpp
+  # Let conda set these
+  sed -i.bak 's/-mmacosx-version-min=10.15//g' Makefile
+  sed -i.bak 's/-mmacosx-version-min=11//g' Makefile
 fi
 
 # Set flags conditionally based on the OS type
diff --git a/recipes/gw/conda_build_config.yaml b/recipes/gw/conda_build_config.yaml
index 90ff7dab2c6f3..1fa9eba4fd39a 100644
--- a/recipes/gw/conda_build_config.yaml
+++ b/recipes/gw/conda_build_config.yaml
@@ -1,4 +1,12 @@
-MACOSX_DEPLOYMENT_TARGET:  # [osx and x86_64]
-  - "10.15"                # [osx and x86_64]
-MACOSX_SDK_VERSION:        # [osx and x86_64]
-  - "10.15"                # [osx and x86_64]
+#MACOSX_DEPLOYMENT_TARGET:  # [osx and x86_64]
+#  - "10.15"                # [osx and x86_64]
+
+#MACOSX_SDK_VERSION:        # [osx and x86_64]
+#  - "10.15"                # [osx and x86_64]
+
+#CFLAGS:
+#  - "-mmacosx-version-min=10.15"  # [osx and x86_64]
+#CXXFLAGS:
+#  - "-mmacosx-version-min=10.15"  # [osx and x86_64]
+#LDFLAGS:
+#  - "-mmacosx-version-min=10.15"  # [osx and x86_64]
diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml
index decc50a9fcd20..43a534a6e6384 100644
--- a/recipes/gw/meta.yaml
+++ b/recipes/gw/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.1.0" %}
-{% set sha256 = "dc96521b8252bde02d9cc68bb3cee156c0469889d2783ee72682338d10657892" %}
+{% set version = "1.1.1" %}
+{% set sha256 = "5ac0430d9179d1a48938f24011c329fe807e72aba0c20eb191c566d129115f86" %}
 
 package:
   name: gw
@@ -31,6 +31,7 @@ build:
     - zlib            # [osx]
     - libuuid
     - libdeflate
+  skip: true  # [osx and x86_64]
 
 requirements:
   build:
@@ -72,7 +73,10 @@ requirements:
 
 test:
   commands:
-    - gw hg19 -b https://github.com/kcleal/gw/releases/download/v1.0.0/demo1.bam -r chr8:37047270-37055161 -n > test.png; ls -lh test.png
+    - which gw && ls -lh $(which gw)
+    - uname -a
+    - if [[ "$(uname)" == "Darwin" ]]; then file $(which gw); otool -L $(which gw); nm $(which gw); fi
+    - gw --version
 
 about:
   home: https://github.com/kcleal/gw
diff --git a/recipes/hatchet/meta.yaml b/recipes/hatchet/meta.yaml
index ea4293e5a40ff..99adcd230e6d9 100755
--- a/recipes/hatchet/meta.yaml
+++ b/recipes/hatchet/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hatchet" %}
-{% set version = "2.0.1" %}
+{% set version = "2.1.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   - url: https://github.com/raphael-group/{{ name }}/archive/v{{ version }}.tar.gz
-    sha256: e8ca462fc4404bacc97b2195e734cd6086eebd40e7941d450c069967d294d988
+    sha256: 979dded4450134ff023f4a7ffbdb6d0d175ac7567e89ab4045c2e12706c3827d
 
   - url: https://packages.gurobi.com/9.0/gurobi9.0.2_linux64.tar.gz  # [not osx]
     sha256: 6527581aef11c3e425c52993d108861ef53ec13971d9931861bf9c88d9d111f3  # [not osx]
@@ -17,7 +17,7 @@ source:
     sha256: 1d58586f9a33ac7035f51f6a04707248218f70bddbec78cb83f11c986ac652cd  # [osx]
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 37]
   entry_points:
     - hatchet = hatchet.__main__:main
@@ -39,6 +39,7 @@ requirements:
     - hmmlearn
     - matplotlib-base
     - mosdepth
+    - numpy <2
     - pandas
     - picard-slim
     - psutil
diff --git a/recipes/hictk/build.sh b/recipes/hictk/build.sh
index dcf141266bc79..1733bcd77a792 100755
--- a/recipes/hictk/build.sh
+++ b/recipes/hictk/build.sh
@@ -2,7 +2,7 @@
 
 export CONAN_NON_INTERACTIVE=1
 
-export CMAKE_BUILD_PARALLEL_LEVEL=1 # ${CPU_COUNT}
+export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
 export CTEST_PARALLEL_LEVEL=${CPU_COUNT}
 
 if [[ ${DEBUG_C} == yes ]]; then
@@ -19,23 +19,31 @@ trap "rm -rf '$scratch'" EXIT
 
 declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
+  # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
   CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
   conan_profile='apple-clang'
+
+  # https://github.com/conda/conda-build/issues/4392
+  for toolname in "otool" "install_name_tool"; do
+    tool=$(find "${BUILD_PREFIX}/bin/" -name "*apple*-$toolname")
+    mv "${tool}" "${tool}.bak"
+    ln -s "/Library/Developer/CommandLineTools/usr/bin/${toolname}" "$tool"
+  done
 else
   CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
-  conan_profile='gcc'
+  conan_profile='clang'
 fi
 
 # Remember to update these profiles when bioconda's compiler toolchains are updated
 mkdir -p "$CONAN_HOME/profiles/"
 ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/$conan_profile"
 
-# Remove unnecessary dependencies from conanfile.txt
-patch conanfile.py < "${RECIPE_DIR}/conanfile.py.patch"
+# Remove unnecessary dependencies from conanfile.py
+patch conanfile.Dockerfile.py < "${RECIPE_DIR}/conanfile.Dockerfile.py.patch"
 
 # Install header-only deps
-conan install conanfile.py \
+conan install conanfile.Dockerfile.py \
        --build="*" \
        -pr:b "$conan_profile" \
        -pr:h "$conan_profile" \
@@ -52,6 +60,7 @@ cmake -DCMAKE_BUILD_TYPE="$CMAKE_BUILD_TYPE"   \
       -DBUILD_SHARED_LIBS=ON                   \
       -DENABLE_DEVELOPER_MODE=OFF              \
       -DHICTK_ENABLE_TESTING=ON                \
+      -DHICTK_ENABLE_FUZZY_TESTING=OFF         \
       -DHICTK_BUILD_EXAMPLES=OFF               \
       -DHICTK_BUILD_BENCHMARKS=OFF             \
       -DHICTK_BUILD_TOOLS=ON                   \
@@ -66,10 +75,9 @@ cmake -DCMAKE_BUILD_TYPE="$CMAKE_BUILD_TYPE"   \
 cmake --build build/
 
 ctest --test-dir build/   \
-      --schedule-random   \
       --output-on-failure \
       --no-tests=error    \
-      --timeout 100
+      --timeout 180
 
 cmake --install build/
 
diff --git a/recipes/hictk/conan_profiles/clang b/recipes/hictk/conan_profiles/clang
new file mode 100644
index 0000000000000..9ee58cee260e2
--- /dev/null
+++ b/recipes/hictk/conan_profiles/clang
@@ -0,0 +1,8 @@
+[settings]
+arch=x86_64
+build_type=Release
+compiler=clang
+compiler.cppstd=17
+compiler.libcxx=libstdc++11
+compiler.version=18
+os=Linux
diff --git a/recipes/hictk/conanfile.Dockerfile.py.patch b/recipes/hictk/conanfile.Dockerfile.py.patch
new file mode 100644
index 0000000000000..63567337cee20
--- /dev/null
+++ b/recipes/hictk/conanfile.Dockerfile.py.patch
@@ -0,0 +1,66 @@
+diff --git a/conanfile.Dockerfile.py b/conanfile.Dockerfile.py
+index c9e6d177..b190d2df 100644
+--- a/conanfile.Dockerfile.py
++++ b/conanfile.Dockerfile.py
+@@ -36,26 +36,10 @@ class HictkConan(ConanFile):
+ 
+     def requirements(self):
+         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+-        self.requires("bzip2/1.0.8#d00dac990f08d991998d624be81a9526")
+-        self.requires("cli11/2.4.2#1b431bda2fb2cd3efed633899abcd8cc")
+         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+-        self.requires("fast_float/6.1.5#e067b96a6271d1b4c255858ca9805bdd")
+-        self.requires("fmt/11.0.2#5c7438ef4d5d69ab106a41e460ce11f3", force=True)
+-        self.requires("hdf5/1.14.4.3#df1467d7374938c231edbe10e83f2bb4", force=True)
+-        self.requires("highfive/2.10.0#3d1bd25944a57fa1bc30a0a22923d528")
+-        self.requires("libarchive/3.7.6#11e70b88b334f684eb9f6b65f287c81e")
+-        self.requires("libdeflate/1.22#f95aebe763153ccbc4cc76c023e42e5a")
+-        self.requires("lz4/1.10.0#68a01ece147a441b463d8cefea68d555", force=True)
+-        self.requires("lzo/2.10#5725914235423c771cb1c6b607109b45")
+-        self.requires("nlohmann_json/3.11.3#45828be26eb619a2e04ca517bb7b828d")
+         self.requires("parallel-hashmap/1.4.0#36ac84df77219748440cdb0f23624d56")
+         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
+         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
+-        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
+-        self.requires("tomlplusplus/3.4.0#85dbfed71376fb8dc23cdcc0570e4727")
+-        self.requires("xz_utils/5.4.5#b885d1d79c9d30cff3803f7f551dbe66")
+-        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+-        self.requires("zlib/1.3.1#f52e03ae3d251dec704634230cd806a2")
+ 
+     def validate(self):
+         if self.settings.get_safe("compiler.cppstd"):
+@@ -64,34 +48,3 @@ class HictkConan(ConanFile):
+     def configure(self):
+         if self.settings.compiler in ["clang", "gcc"]:
+             self.settings.compiler.libcxx = "libstdc++11"
+-
+-        self.options["fmt"].header_only = True
+-        self.options["hdf5"].enable_cxx = False
+-        self.options["hdf5"].hl = False
+-        self.options["hdf5"].threadsafe = False
+-        self.options["hdf5"].parallel = False
+-        self.options["highfive"].with_boost = False
+-        self.options["highfive"].with_eigen = False
+-        self.options["highfive"].with_opencv = False
+-        self.options["highfive"].with_xtensor = False
+-        self.options["libarchive"].with_acl = False
+-        self.options["libarchive"].with_zlib = True
+-        self.options["libarchive"].with_bzip2 = True
+-        self.options["libarchive"].with_libxml2 = False
+-        self.options["libarchive"].with_expat = False
+-        self.options["libarchive"].with_iconv = False
+-        self.options["libarchive"].with_acl = False
+-        self.options["libarchive"].with_pcreposix = False
+-        self.options["libarchive"].with_cng = False
+-        self.options["libarchive"].with_nettle = False
+-        self.options["libarchive"].with_openssl = False
+-        self.options["libarchive"].with_libb2 = False
+-        self.options["libarchive"].with_lz4 = True
+-        self.options["libarchive"].with_lzo = True
+-        self.options["libarchive"].with_lzma = True
+-        self.options["libarchive"].with_zstd = True
+-        self.options["libarchive"].with_mbedtls = False
+-        self.options["libarchive"].with_xattr = False
+-        self.options["libarchive"].with_pcre2 = False
+-        self.options["spdlog"].header_only = True
+-        self.options["zstd"].build_programs = False
diff --git a/recipes/hictk/conanfile.py.patch b/recipes/hictk/conanfile.py.patch
deleted file mode 100644
index 78d2295831839..0000000000000
--- a/recipes/hictk/conanfile.py.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-diff --git a/conanfile.py b/conanfile.py
-index 29fc114..93f6940 100644
---- a/conanfile.py
-+++ b/conanfile.py
-@@ -36,23 +36,11 @@ class HictkConan(ConanFile):
-         return 17
- 
-     def requirements(self):
--        self.requires("arrow/16.1.0#f484da4c4c27c1eb3ead5d61b70635cd")
--        self.requires("boost/1.85.0#d9ae7996a5b917e0cfd4b738aa976dee", force=True)
-         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
--        self.requires("catch2/3.6.0#819bc5a82c2cb626916fc18ee1dbc45f")
--        self.requires("cli11/2.4.2#1b431bda2fb2cd3efed633899abcd8cc")
-         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
--        self.requires("eigen/3.4.0#2e192482a8acff96fe34766adca2b24c")
--        self.requires("fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e")
--        self.requires("fmt/10.2.1#9199a7a0611866dea5c8849a77467b25")
--        self.requires("hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1")
--        self.requires("highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5")
--        self.requires("libdeflate/1.20#3bd86e0160becf992346aa68b4938c40")
-         self.requires("parallel-hashmap/1.3.12#dc7755096d8a1fac7792fdd85760b6ca")
-         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
-         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
--        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
--        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b")
- 
-     def validate(self):
-         if self.settings.get_safe("compiler.cppstd"):
-@@ -61,61 +49,3 @@ class HictkConan(ConanFile):
-     def configure(self):
-         if self.settings.compiler in ["clang", "gcc"]:
-             self.settings.compiler.libcxx = "libstdc++11"
--
--        self.options["arrow"].compute = True
--        self.options["arrow"].parquet = False
--        self.options["arrow"].with_boost = True
--        self.options["arrow"].with_re2 = True
--        self.options["arrow"].with_thrift = False
--        self.options["boost"].system_no_deprecated = True
--        self.options["boost"].asio_no_deprecated = True
--        self.options["boost"].filesystem_no_deprecated = True
--        self.options["boost"].filesystem_version = 4
--        self.options["boost"].zlib = False
--        self.options["boost"].bzip2 = False
--        self.options["boost"].lzma = False
--        self.options["boost"].zstd = False
--        self.options["boost"].without_atomic = False
--        self.options["boost"].without_charconv = True
--        self.options["boost"].without_chrono = True
--        self.options["boost"].without_container = True
--        self.options["boost"].without_context = True
--        self.options["boost"].without_contract = True
--        self.options["boost"].without_coroutine = True
--        self.options["boost"].without_date_time = True
--        self.options["boost"].without_exception = True
--        self.options["boost"].without_fiber = True
--        self.options["boost"].without_filesystem = False
--        self.options["boost"].without_graph = True
--        self.options["boost"].without_graph_parallel = True
--        self.options["boost"].without_iostreams = True
--        self.options["boost"].without_json = True
--        self.options["boost"].without_locale = True
--        self.options["boost"].without_log = True
--        self.options["boost"].without_math = True
--        self.options["boost"].without_mpi = True
--        self.options["boost"].without_nowide = True
--        self.options["boost"].without_program_options = True
--        self.options["boost"].without_python = True
--        self.options["boost"].without_random = True
--        self.options["boost"].without_regex = True
--        self.options["boost"].without_serialization = True
--        self.options["boost"].without_stacktrace = True
--        self.options["boost"].without_system = False
--        self.options["boost"].without_test = True
--        self.options["boost"].without_thread = True
--        self.options["boost"].without_timer = True
--        self.options["boost"].without_type_erasure = True
--        self.options["boost"].without_url = True
--        self.options["boost"].without_wave = True
--        self.options["fmt"].header_only = True
--        self.options["hdf5"].enable_cxx = False
--        self.options["hdf5"].hl = False
--        self.options["hdf5"].threadsafe = False
--        self.options["hdf5"].parallel = False
--        self.options["highfive"].with_boost = False
--        self.options["highfive"].with_eigen = False
--        self.options["highfive"].with_opencv = False
--        self.options["highfive"].with_xtensor = False
--        self.options["spdlog"].header_only = True
--        self.options["zstd"].build_programs = False
diff --git a/recipes/hictk/conda_build_config.yaml b/recipes/hictk/conda_build_config.yaml
new file mode 100644
index 0000000000000..3397464cf13fd
--- /dev/null
+++ b/recipes/hictk/conda_build_config.yaml
@@ -0,0 +1,8 @@
+c_compiler:             # [linux]
+  - clang               # [linux]
+c_compiler_version:     # [linux]
+  - 18                  # [linux]
+cxx_compiler:           # [linux]
+  - clangxx             # [linux]
+cxx_compiler_version:   # [linux]
+  - 18                  # [linux]
diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml
index 42a5eb4d57b4a..05f98f4ea3b16 100644
--- a/recipes/hictk/meta.yaml
+++ b/recipes/hictk/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "hictk" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "e337f52658a257eb6265e211dd3cef6b73db40bdc5b5a6433b47ce4faa6006fb" %}
+{% set version = "2.0.1" %}
+{% set sha256 = "bd12f87f6f33ea91f898d6b660e8dcca9f97b0aaf27719e867ab643cd705fced" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('hictk', max_pin='x') }}
 
@@ -22,24 +22,28 @@ requirements:
     - cmake >=3.25
     - conan >=2
     - make
-    - catch2 >=3.5
-    - cli11 >=2.3
+    - catch2 >=3.7
+    - cli11 >=2.4
     - eigen >=3.4
-    - fast_float >=5
-    - fmt >=10
-    - highfive >=2.8
-    - spdlog >=1.12
+    - fast_float >=6
+    - fmt >=11
+    - highfive >=2.9
+    - nlohmann_json >=3.11
+    - tomlplusplus >=3.3
+    - spdlog >=1.14
 
   host:
     - hdf5 >=1.12
+    - libarchive >=3
     - libarrow >=16
-    - libdeflate
+    - libdeflate >=1
     - zstd >=1.5
 
   run:
     - hdf5 >=1.12
+    - libarchive >=3
     - libarrow >=16
-    - libdeflate
+    - libdeflate >=1
     - zstd >=1.5
 
 about:
@@ -48,45 +52,18 @@ about:
   license_file: LICENSE
   summary: Blazing fast toolkit to work with .hic and .cool files
   dev_url: https://github.com/paulsengroup/{{ name }}
-  doc_url: https://github.com/paulsengroup/{{ name }}#readme
+  doc_url: https://{{ name }}.readthedocs.io/en/stable/
 
 test:
   requires:
+    - python >=3.11,<3.13
+    - pip
     - curl
-    - cooler>=0.9.3
     - perl-digest-sha1
-    - xz
+    - zstd
   source_files:
     - cmake/FetchTestDataset.cmake
-    - test/scripts/check_test_files_exist.sh
-    - test/scripts/compare_matrix_files.sh
-    - test/scripts/compare_plain_files.sh
-    - test/scripts/compare_weights.py
-    - test/scripts/hictk_balance_ice.sh
-    - test/scripts/hictk_balance_scale.sh
-    - test/scripts/hictk_balance_vc.sh
-    - test/scripts/hictk_convert_hic2cool.sh
-    - test/scripts/hictk_convert_cool2hic.sh
-    - test/scripts/hictk_dump_cells.sh
-    - test/scripts/hictk_dump_normalizations.sh
-    - test/scripts/hictk_dump_resolutions.sh
-    - test/scripts/hictk_dump_chroms.sh
-    - test/scripts/hictk_dump_bins.sh
-    - test/scripts/hictk_dump_gw.sh
-    - test/scripts/hictk_dump_cis.sh
-    - test/scripts/hictk_dump_trans.sh
-    - test/scripts/hictk_dump_balanced.sh
-    - test/scripts/hictk_fix_mcool.sh
-    - test/scripts/hictk_load_coo.sh
-    - test/scripts/hictk_load_bg2.sh
-    - test/scripts/hictk_load_4dn.sh
-    - test/scripts/hictk_merge.sh
-    - test/scripts/hictk_rename_chromosomes.sh
-    - test/scripts/hictk_validate.sh
-    - test/scripts/hictk_zoomify.sh
-    - test/scripts/nproc.sh
-    - test/scripts/readlink.sh
-    - test/scripts/shuffle.sh
+    - test/integration/
   commands:
     - hictk --help
     - hictk --version
diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh
index 40324b44eca22..1dbc027508faa 100755
--- a/recipes/hictk/run_test.sh
+++ b/recipes/hictk/run_test.sh
@@ -5,45 +5,37 @@ set -u
 set -x
 set -o pipefail
 
+which hictk
+if [[ "$OSTYPE" =~ .*darwin.* ]]; then
+  otool -L "$(which hictk)"
+else
+  ldd  "$(which hictk)"
+fi
+
+hictk --version
+
 # Extract test dataset URL and checksum
 url="$(grep -F 'DOWNLOAD' 'cmake/FetchTestDataset.cmake' | sed -E 's/.*DOWNLOAD[[:space:]]+//')"
 checksum="$(grep -F 'EXPECTED_HASH' 'cmake/FetchTestDataset.cmake' | sed 's/.*SHA256=//')"
 
 # Download and extract test datasets
-curl -L "$url" -o hictk_test_dataset.tar.xz
-echo "$checksum  hictk_test_dataset.tar.xz" > checksum.sha256
+curl -L "$url" -o hictk_test_dataset.tar.zst
+echo "$checksum  hictk_test_dataset.tar.zst" > checksum.sha256
 shasum -c checksum.sha256
 
-tar -xf hictk_test_dataset.tar.xz
+zstdcat hictk_test_dataset.tar.zst | tar -xf -
 
-hictk="$(which hictk)"
+# Install the test suite
+pip install test/integration
 
 # Run integration tests
-
-test/scripts/hictk_balance_ice.sh "$hictk"
-test/scripts/hictk_balance_scale.sh "$hictk"
-test/scripts/hictk_balance_vc.sh "$hictk"
-
-test/scripts/hictk_dump_chroms.sh "$hictk"
-test/scripts/hictk_dump_bins.sh "$hictk"
-test/scripts/hictk_dump_gw.sh "$hictk"
-test/scripts/hictk_dump_cis.sh "$hictk"
-test/scripts/hictk_dump_trans.sh "$hictk"
-test/scripts/hictk_dump_balanced.sh "$hictk"
-
-test/scripts/hictk_convert_hic2cool.sh "$hictk"
-test/scripts/hictk_convert_cool2hic.sh "$hictk"
-
-test/scripts/hictk_load_coo.sh "$hictk" sorted
-test/scripts/hictk_load_coo.sh "$hictk" unsorted
-test/scripts/hictk_load_bg2.sh "$hictk" sorted
-test/scripts/hictk_load_bg2.sh "$hictk" unsorted
-test/scripts/hictk_load_4dn.sh "$hictk"
-
-test/scripts/hictk_merge.sh "$hictk"
-
-test/scripts/hictk_rename_chromosomes.sh "$hictk"
-
-test/scripts/hictk_validate.sh "$hictk"
-
-test/scripts/hictk_zoomify.sh "$hictk"
+hictk_integration_suite \
+  "$(which hictk)" \
+  test/integration/config.toml \
+  --data-dir test/data \
+  --do-not-copy-binary \
+  --threads "${CPU_COUNT}" \
+  --result-file results.json
+
+printf '#####\n#####\n#####\n\n\n'
+cat results.json
diff --git a/recipes/hifiasm/meta.yaml b/recipes/hifiasm/meta.yaml
index 404d3f626204f..b9217bc40ec06 100644
--- a/recipes/hifiasm/meta.yaml
+++ b/recipes/hifiasm/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.19.9" %}
+{% set version = "0.20.0" %}
 
 package:
   name: hifiasm
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/chhylp123/hifiasm/archive/{{ version }}.tar.gz
-  sha256: 8b80c03ad50b65e197d7e633740a135ad1202949ebfe4dfb977f27f2f2ae83ee
+  sha256: 24a0cc99dd3f40f74a8a975a3f7b70e378ee6c4c90d1b28d7ed979afaec101ab
   patches:
     - linux-aarch64-support.patch
 
diff --git a/recipes/hificnv/meta.yaml b/recipes/hificnv/meta.yaml
index e6d3537158283..77b7d6262955c 100644
--- a/recipes/hificnv/meta.yaml
+++ b/recipes/hificnv/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "hificnv" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "276afe35d34171f17a5f30e7aa35eb156765156536ae7411171376565d63cfe5" %}
+{% set version = "1.0.1" %}
+{% set sha256 = "3f5c32cbf46ac8aacaa6ac5984e6b8678779a177201cf50c354fb904750f9376" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml
index d4752768e5416..2084feff2576c 100644
--- a/recipes/hybracter/meta.yaml
+++ b/recipes/hybracter/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hybracter" %}
-{% set version = "0.9.1" %}
+{% set version = "0.10.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz
-  sha256: e5f71934901552d4c26a3be0cae71982001ed866af0c27fe2da8432b08d395ad
+  sha256: 6640aacea33671c2bf1714693ecdd48c87a708d8bbf0ad1f964ddd6fc34e0224
 
 build:
   number: 0
   noarch: python
   entry_points:
     - hybracter=hybracter.__main__:main
-  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   run_exports:
     - {{ pin_subpackage('hybracter', max_pin="x") }}
 
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - snakemake-minimal >=7.14.0
@@ -37,12 +38,13 @@ test:
     - hybracter --help
 
 about:
-  home: https://github.com/gbouras13/hybracter
-  summary: An automated long-read first bacterial genome assembly pipeline.
+  home: "https://github.com/gbouras13/hybracter"
+  summary: "An automated long-read first bacterial genome assembly pipeline."
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  doc_url: https://hybracter.readthedocs.io/en/latest/
+  doc_url: "https://hybracter.readthedocs.io/en/latest"
+  dev_url: "https://github.com/gbouras13/hybracter"
 
 extra:
   recipe-maintainers:
diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml
index b531a053fb8a8..ee2bf7b0f2ff3 100644
--- a/recipes/hyphy/meta.yaml
+++ b/recipes/hyphy/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "2.5.62" %}
-{% set sha256 = "8b98ef1d69f1a985026282d644e5df022bd22c1e2614f9d8348377f291e7f9e8" %}
+{% set version = "2.5.63" %}
+{% set sha256 = "86a94a601fa136443a8cd69f61e3a47b1dc85f10743d317715b1e433278e9ee0" %}
 
 package:
   name: hyphy
@@ -10,7 +10,7 @@ source:
   sha256: '{{ sha256 }}'
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage("hyphy", max_pin="x.x") }}
 requirements:
diff --git a/recipes/icfree-ml/meta.yaml b/recipes/icfree-ml/meta.yaml
index d0e9659d2aa05..09c13b468f85f 100644
--- a/recipes/icfree-ml/meta.yaml
+++ b/recipes/icfree-ml/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "icfree-ml" %}
-{% set version = "2.5.0" %}
+{% set version = "2.5.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.5.0.tar.gz
-  sha256: 9720880aba7613b582cd519749c5908195679e228a196cbc6ae941814410aef3
+  url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.5.1.tar.gz
+  sha256: 4c62b4ee55d77a8af8d277ae1b58b0df2c977ca39aead9188ede7ae061a8f18d
 
 build:
   number: 0
diff --git a/recipes/inmoose/meta.yaml b/recipes/inmoose/meta.yaml
new file mode 100644
index 0000000000000..241dd6ba98d54
--- /dev/null
+++ b/recipes/inmoose/meta.yaml
@@ -0,0 +1,64 @@
+{% set name = "inmoose" %}
+{% set version = "0.7.2" %}
+{% set sha256 = "e7e16d0d20335476f66a24158f26cbadac4f1c8244684441f5b2451c1ae3c8b7" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/epigenelabs/inmoose/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [py < 39]
+  run_exports:
+    - {{ pin_subpackage('inmoose', max_pin="x.x") }}
+  script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-cache-dir --no-build-isolation"
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - python
+    - pip
+    - setuptools
+    - cython >=3.0.0
+    - numpy >=2.0.0
+    - scipy
+  run:
+    - python
+    - numpy
+    - scipy
+    - pandas
+    - seaborn-base
+    - matplotlib-base
+    - anndata
+    - scikit-learn
+    - fastcluster
+    - mpmath >=1.1.0
+    - patsy
+    - statsmodels
+    - click
+
+test:
+  imports:
+    - inmoose
+    - inmoose.pycombat
+    - inmoose.consensus_clustering.consensus_clustering
+
+about:
+  home: https://github.com/epigenelabs/inmoose
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: LICENSE
+  summary: 'InMoose is the Integrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.'
+  dev_url: https://github.com/epigenelabs/inmoose
+
+extra:
+  container:
+    # click requires a unicode locale when used with Python 3
+    # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
+    extended-base: true  # [py3k]
diff --git a/recipes/irma/irma-check-dir-writable.patch b/recipes/irma/irma-check-dir-writable.patch
index 57996031884e8..1863419908120 100644
--- a/recipes/irma/irma-check-dir-writable.patch
+++ b/recipes/irma/irma-check-dir-writable.patch
@@ -1,11 +1,11 @@
---- IRMA	2022-05-09 15:15:26.345377197 -0500
-+++ IRMA	2022-05-09 15:19:18.818708355 -0500
-@@ -111,7 +111,7 @@
+--- IRMA	2024-09-24 17:47:20.000000000 +0200
++++ IRMA	2024-10-21 18:16:45.067579652 +0200
+@@ -141,7 +141,7 @@
  
  # make sure output directory is valid
- if [ ! -w "$destination_directory" ];then 
--	abort "output directory not writable: $destination_directory"
-+  timestamp "WARNING: output directory may not be writable: $destination_directory"
+ if [ ! -w "$destination_directory" ]; then
+-    abort "output directory not writable: $destination_directory"
++    timestamp "WARNING: output directory may not be writable: $destination_directory"
  fi
  
  # test input files
diff --git a/recipes/irma/irma-fix-bin-cmds.patch b/recipes/irma/irma-fix-bin-cmds.patch
index 6e85b5d064f08..59e46b5a22c91 100644
--- a/recipes/irma/irma-fix-bin-cmds.patch
+++ b/recipes/irma/irma-fix-bin-cmds.patch
@@ -1,6 +1,6 @@
---- IRMA	2021-03-11 13:45:41.000000000 -0600
-+++ IRMA	2021-06-04 16:18:36.088939674 -0500
-@@ -140,14 +140,14 @@
+--- IRMA	2024-02-21 18:55:07.000000000 +0100
++++ IRMA	2024-10-21 10:52:21.634249943 +0200
+@@ -172,14 +172,14 @@
  check_prgm Rscript
  check_prgm perl
  
@@ -18,14 +18,13 @@
 -BASH=bash
 +RSCRIPT="Rscript"
 +BASH="bash"
+ MERGESAMPAIRS=("$spath/mergeSAMpairs.pl")
+ FASTQ_CONVERTER=("$spath/fastQ_converter.pl")
  
- # select cat for reading reads
- if [ "${#LEFT}" -gt "2" ];then
-@@ -204,14 +204,19 @@
- 		exit 0
- 	fi
+@@ -267,14 +267,18 @@
+     fi
  fi
-+
+ 
 +if [ -r "./irma_config.sh" ]; then
 +    echo "Loading config file 'irma_config.sh'"
 +    source "./irma_config.sh"
@@ -33,15 +32,15 @@
 +    echo "No user config file 'irma_config.sh' specified."
 +fi
 +
- [ ! -z "$LFASTM" ] && SECONDARY_SORT=$LFASTM
+ [ -n "$LFASTM" ] && SECONDARY_SORT=$LFASTM
  REF1_SET=$REF_SET
  
  # selection of zip utility
--if command -v "$spath"/pigz_$OS >/dev/null 2>&1;then
--	ZIP="$spath"/pigz_$OS
--	Z_OPTS="-p $DOUBLE_LOCAL_PROC -4"
--elif command -v pigz >/dev/null 2>&1;then
+-if command -v "$spath"/pigz_$OS > /dev/null 2>&1; then
+-    ZIP="$spath"/pigz_$OS
+-    Z_OPTS="-p $DOUBLE_LOCAL_PROC -4"
+-elif command -v pigz > /dev/null 2>&1; then
 +if command -v "pigz" >/dev/null 2>&1;then
- 	ZIP="pigz"
- 	Z_OPTS="-p $DOUBLE_LOCAL_PROC -4"
- elif command -v gzip >/dev/null 2>&1;then
+     ZIP="pigz"
+     Z_OPTS="-p $DOUBLE_LOCAL_PROC -4"
+ elif command -v gzip > /dev/null 2>&1; then
diff --git a/recipes/irma/label-fix-bin-cmds.patch b/recipes/irma/label-fix-bin-cmds.patch
index 99a88fd168e61..235f8ee085b3a 100644
--- a/recipes/irma/label-fix-bin-cmds.patch
+++ b/recipes/irma/label-fix-bin-cmds.patch
@@ -1,6 +1,6 @@
---- flu-amd/LABEL	2021-03-11 13:45:48.000000000 -0600
-+++ LABEL	2021-06-04 16:40:06.961358066 -0500
-@@ -253,11 +253,11 @@
+--- orig_flu-amd-202408/flu-amd/LABEL	2024-09-24 17:47:17.000000000 +0200
++++ my_flu-amd-202408/flu-amd/LABEL	2024-10-21 18:28:27.096784464 +0200
+@@ -250,10 +250,10 @@
  bin="$bpath"/$resources/scripts
  hmmscore="$bin"/hmmscore_$OS
  align2model="$bin"/align2model_$OS
@@ -8,10 +8,9 @@
 -FastTreeMP="$bin"/FastTreeMP_$OS
 +muscle="muscle"
 +FastTreeMP="FastTreeMP"
- modelfromalign="$bin"/modelfromalign_$OS
  shogun="$bin"/shogun_$OS
 -PARALLEL="$bin/parallel"
 +PARALLEL="parallel"
  
- 
- if [ "$DO_WEB" -eq "0" ];then
+ if [ "$DO_WEB" -eq "0" ]; then
+     tpath="$bpath"/$resources/test_data
diff --git a/recipes/irma/meta.yaml b/recipes/irma/meta.yaml
index 3e1a180a3615e..5760801579ebb 100644
--- a/recipes/irma/meta.yaml
+++ b/recipes/irma/meta.yaml
@@ -1,15 +1,13 @@
 {% set name = "IRMA" %}
-{% set version = "1.0.3" %}
-{% set hash_type = "sha256" %}
-{% set hash_value = "c5f6b452e1a6cfa8dcb02d1646c9e30e071557327a7cf11cab91a9b92e0eb455" %}
+{% set version = "1.2.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://wonder.cdc.gov/amd/flu/irma/flu-amd-202209.zip
-  {{ hash_type }}: {{ hash_value }}
+  url: https://wonder.cdc.gov/amd/flu/irma/flu-amd-202408.zip
+  sha256: 8cc113289f3b441ef2bd8f7d793f6be71fbb77babbfff022e187ba2463fce9f8
   patches:
     - irma-fix-bin-cmds.patch
     - label-fix-bin-cmds.patch
@@ -18,6 +16,8 @@ source:
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('irma', max_pin="x.x") }}
 
 requirements:
   host:
diff --git a/recipes/iseq/meta.yaml b/recipes/iseq/meta.yaml
index 193270e7e7cef..478271bd01ce4 100644
--- a/recipes/iseq/meta.yaml
+++ b/recipes/iseq/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "iSeq" %}
-{% set version = "1.1.0" %}
+{% set version = "1.2.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,23 +7,23 @@ package:
 
 source:
   url: https://github.com/BioOmics/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: de0b9f1e06842a14f0a112023b989a38f6d422d860d44b19d3ec717d3c00bc34
+  sha256: 9ddac60c63f774aac274de5a2abb1917774499c56f3c233aa19abe22f053fef3
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 requirements:
-  build:
+  host:
     - bash
   run:
     - pigz
     - wget
     - axel
     - aspera-cli
-    - sra-tools =2.11.0
+    - sra-tools >=2.11.0
 
 test:
   commands:
@@ -32,8 +32,10 @@ test:
 about:
   home: https://github.com/BioOmics/iSeq
   license: MIT
-  summary: "iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases"
+  license_family: MIT
+  summary: "iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases."
+  dev_url: https://github.com/BioOmics/iSeq
 
 extra:
   recipe-maintainers:
-    - Haoyu Chao <haoyuchao@zju.edu.cn>
+    - BioOmics
diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml
index 821dfee562371..077e3f555dfcc 100644
--- a/recipes/jbrowse2/meta.yaml
+++ b/recipes/jbrowse2/meta.yaml
@@ -1,12 +1,12 @@
 # When updating, check the @jbrowse/cli version in build.sh too
-{% set version = "2.15.4" %}
+{% set version = "2.16.0" %}
 
 package:
   name: jbrowse2
   version: {{ version }}
 
 source:
-  sha256: fa0a6163dab65d1705c1968cc41adc0f6b035a8fbc572b7ddff12721b5b58642
+  sha256: 5f58748cf7c3dcbaddbf87e123cfa878f0d64d3e965bd2ac9bda1b359db40dfd
   url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip
 
 build:
diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml
index f7bd0adb17bd0..f9e4339de96f3 100644
--- a/recipes/kb-python/meta.yaml
+++ b/recipes/kb-python/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "kb-python" %}
-{% set version = "0.28.2" %}
+{% set version = "0.29.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz
-  sha256: e8c910865fd5196b1b3163e18a565ef96c8518b2cf34f87f288dfdc85b339078
+  sha256: f94e20d592dfd6e7d50b470c0d83732bfb34c6f9c822f22714dac0bb98f87aa3
 
 build:
-  number: 2
+  number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - kb=kb_python.main:main
   run_exports:
@@ -20,25 +20,27 @@ build:
 
 requirements:
   host:
-    - python >=3.7, <3.9
+    - python >=3.8
     - pip
+    - setuptools
   run:
-    - python >=3.7, <3.9
-    - anndata >=0.6.22.post1
+    - python >=3.8
+    - anndata >=0.9.2
     - h5py >=2.10.0
     - jinja2 >2.10.1
     - loompy >=3.0.6
     - nbconvert >=5.6.0
     - nbformat >=4.4.0
-    - ngs-tools >=1.5.11
+    - ngs-tools >=1.8.6
     - numpy >=1.17.2
-    - pandas >=1.0.0, <2
+    - pandas >=1.5.3
     - plotly >=4.5.0
     - scanpy >=1.4.4.post1
     - scikit-learn >=0.21.3
     - tqdm >=4.39.0
     - requests >=2.22.0
     - typing-extensions >=3.7.4
+    - biopython >=1.8
 
 test:
   commands:
@@ -51,10 +53,12 @@ about:
   license: BSD-2-Clause
   license_file: LICENSE
   license_family: BSD
-  summary: "A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing"
+  summary: "A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing."
   dev_url: https://github.com/pachterlab/kb_python
-  doc_url: https://www.kallistobus.tools/
+  doc_url: https://www.kallistobus.tools
 
 extra:
   recipe-maintainers:
     - Maarten-vd-Sande
+  identifiers:
+    - doi:10.1101/2023.11.21.568164
diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml
index e4ced42950a1a..1421ee6fad184 100644
--- a/recipes/last/meta.yaml
+++ b/recipes/last/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "LAST" %}
-{% set version = "1584" %}
+{% set version = "1595" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.tar.gz"
-  sha256: 5ed143d7311a1e2ea1fe2be87a2484612689a1498420e2a454762a6b3ab38ba3
+  sha256: dedc8dbcecd7f134d5c0f64e97c500c1588303235528022a42c3ca74bb22995f
 
 build:
   number: 0
diff --git a/recipes/lofreq/0001-patches b/recipes/lofreq/0001-patches
new file mode 100644
index 0000000000000..c711d24f51e11
--- /dev/null
+++ b/recipes/lofreq/0001-patches
@@ -0,0 +1,260 @@
+diff --git a/configure.ac b/configure.ac
+index ec939f5..13494a5 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -146,11 +146,12 @@ AX_PTHREAD([
+         AC_MSG_ERROR([No pthread support on this machine]))
+ #AX_PTHREAD()
+ 
+-
+-# explicit libm check
++# if any of these sit in unusual places use
++# export LDFLAGS="-L$path" before calling configure
+ AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm]))
+ AC_CHECK_LIB(z, gzread,, AC_MSG_ERROR([Could not find libz]))
+-
++AC_CHECK_LIB([gslcblas],[cblas_dgemm])
++AC_CHECK_LIB(gsl, gsl_cdf_poisson_P,, AC_MSG_WARN([libgsl not found. Not using fast approximation]))
+ 
+ # http://www.gnu.org/software/automake/manual/html_node/Python.html
+ AM_PATH_PYTHON([2.7])
+diff --git a/src/lofreq/Makefile.am b/src/lofreq/Makefile.am
+index 102076b..b7c71cf 100644
+--- a/src/lofreq/Makefile.am
++++ b/src/lofreq/Makefile.am
+@@ -1,4 +1,4 @@
+-AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../cdflib90/ -I../uthash $(HTSLIB_CPPFLAGS) @AM_CFLAGS@
++AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -O3 -I../cdflib90/ -I../uthash $(HTSLIB_CPPFLAGS) @AM_CFLAGS@
+ AM_LDFLAGS = $(LDFLAGS_for_htslib) @AM_LDFLAGS@
+ bin_PROGRAMS = lofreq
+ lofreq_SOURCES = bam_md_ext.c bam_md_ext.h \
+@@ -42,3 +42,4 @@ endif
+ 
+ # note: order matters
+ lofreq_LDADD = $(LIBS_for_htslib) ../cdflib90/libcdf.a
++# -l:libgsl.a -lm
+diff --git a/src/lofreq/lofreq_call.c b/src/lofreq/lofreq_call.c
+index 6537a11..81c0c7b 100644
+--- a/src/lofreq/lofreq_call.c
++++ b/src/lofreq/lofreq_call.c
+@@ -315,7 +315,7 @@ call_alt_ins(const plp_col_t *p, double *bi_err_probs, int bi_num_err_probs,
+                bi_num_err_probs, ins_counts[0], ins_counts[1], ins_counts[2]);
+      // compute p-value for insertion
+      if (snpcaller(bi_pvalues, bi_err_probs, bi_num_err_probs, ins_counts,
+-                   conf->bonf_indel, conf->sig)) {
++                   conf->bonf_indel, conf->sig, conf->approx_threshold_n)) {
+           fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                   __FILE__, __FUNCTION__, __LINE__);
+           return 1;
+@@ -380,7 +380,7 @@ int call_alt_del(const plp_col_t *p, double *bd_err_probs, int bd_num_err_probs,
+ 
+      /* snpcaller for deletion */
+      if (snpcaller(bd_pvalues, bd_err_probs, bd_num_err_probs, del_counts,
+-                   conf->bonf_indel, conf->sig)) {
++                   conf->bonf_indel, conf->sig, conf->approx_threshold_n)) {
+           fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                   __FILE__, __FUNCTION__, __LINE__);
+           return 1;
+@@ -803,7 +803,7 @@ call_snvs(const plp_col_t *p, varcall_conf_t *conf)
+                 bc_num_err_probs, alt_counts[0], alt_counts[1], alt_counts[2], num_snv_tests, conf->bonf_subst, conf->sig);
+ 
+       if (snpcaller(pvalues, bc_err_probs, bc_num_err_probs,
+-                   alt_counts, conf->bonf_subst, conf->sig)) {
++                   alt_counts, conf->bonf_subst, conf->sig, conf->approx_threshold_n)) {
+            fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                    __FILE__, __FUNCTION__, __LINE__);
+            free(bc_err_probs);
+@@ -986,6 +986,7 @@ usage(const mplp_conf_t *mplp_conf, const varcall_conf_t *varcall_conf)
+      fprintf(stderr, "       -C | --min-cov INT           Test only positions having at least this coverage [%d]\n", varcall_conf->min_cov);
+      fprintf(stderr, "                                    (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)\n");
+      fprintf(stderr, "       -d | --max-depth INT         Cap coverage at this depth [%d]\n", mplp_conf->max_depth);
++     fprintf(stderr, "       -t | --approx-threshold INT  Use fast approximation at this depth (might decrease number of calls; off if <= 0) [%d]\n", varcall_conf->approx_threshold_n);
+      fprintf(stderr, "            --illumina-1.3          Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded\n");
+      fprintf(stderr, "            --use-orphan            Count anomalous read pairs (i.e. where mate is not aligned properly)\n");
+      fprintf(stderr, "            --plp-summary-only      No variant calling. Just output pileup summary per column\n");
+@@ -1094,6 +1095,7 @@ for cov in coverage_range:
+ 
+               {"min-cov", required_argument, NULL, 'C'},
+               {"max-depth", required_argument, NULL, 'd'},
++              {"approx-threshold", required_argument, NULL, 't'},
+ 
+               {"illumina-1.3", no_argument, &illumina_1_3, 1},
+               {"use-orphan", no_argument, &use_orphan, 1},
+@@ -1272,6 +1274,10 @@ for cov in coverage_range:
+               mplp_conf.max_depth = atoi(optarg);
+               break;
+ 
++         case 't':
++              varcall_conf.approx_threshold_n = atoi(optarg);
++              break;
++
+          case 'h':
+               usage(& mplp_conf, & varcall_conf);
+               return 0; /* WARN: not printing defaults if some args where parsed */
+diff --git a/src/lofreq/lofreq_uniq.c b/src/lofreq/lofreq_uniq.c
+index 53ad137..af03fe4 100644
+--- a/src/lofreq/lofreq_uniq.c
++++ b/src/lofreq/lofreq_uniq.c
+@@ -309,7 +309,7 @@ uniq_snv(const plp_col_t *p, void *confp)
+           alt_counts[1] = alt_counts[2] = 0;
+ 
+           if (snpcaller(pvalues, err_probs, num_err_probs,
+-                        alt_counts, bonf, alpha)) {
++                        alt_counts, bonf, alpha, -1)) {
+                fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                        __FILE__, __FUNCTION__, __LINE__);
+                free(err_probs);
+diff --git a/src/lofreq/plp.c b/src/lofreq/plp.c
+index 808d791..2336445 100644
+--- a/src/lofreq/plp.c
++++ b/src/lofreq/plp.c
+@@ -816,7 +816,11 @@ void compile_plp_col(plp_col_t *plp_col,
+       * n_plp[i] - m
+       */
+      ref_base = (ref && pos < ref_len)? ref[pos] : 'N';
+-
++     /* Added by Ryan Morin in an attempt to mitigate issues with non-ACTG characters in the reference
++     An example position (hg38) affected by this is chr17   83129591  (the reference base is W) */
++     if (! (ref_base == 'A' || ref_base == 'C' || ref_base == 'T' || ref_base == 'G' || ref_base == 'N')){
++          ref_base = 'N';
++     }
+      plp_col_init(plp_col);
+      plp_col->target = strdup(target_name);
+      plp_col->pos = pos;
+@@ -1276,8 +1280,8 @@ check_indel:
+ 
+      for (i = 0; i < NUM_NT4; ++i) {
+           assert(plp_col->fw_counts[i] + plp_col->rv_counts[i] == plp_col->base_quals[i].n);
+-          assert(plp_col->base_quals[i].n == plp_col->baq_quals[i].n);
+-          assert(plp_col->base_quals[i].n == plp_col->map_quals[i].n);
++          /* FIXME only makes sense if BAQ is on assert(plp_col->base_quals[i].n == plp_col->baq_quals[i].n); */
++          /* FIXME only makes sense if MQ is on assert(plp_col->base_quals[i].n == plp_col->map_quals[i].n); */
+           /* assert(plp_col->map_quals[i].n == plp_col->source_quals[i].n);*/
+      }
+ }
+diff --git a/src/lofreq/snpcaller.c b/src/lofreq/snpcaller.c
+index 253430c..f3a8e44 100644
+--- a/src/lofreq/snpcaller.c
++++ b/src/lofreq/snpcaller.c
+@@ -43,6 +43,8 @@
+ #include "fet.h"
+ #include "utils.h"
+ #include "log.h"
++#include "gsl/gsl_randist.h"
++#include "gsl/gsl_cdf.h"
+ 
+ #include "snpcaller.h"
+ #if TIMING
+@@ -635,6 +637,7 @@ init_varcall_conf(varcall_conf_t *c)
+      c->flag |= VARCALL_USE_IDAQ;
+      c->only_indels = 0;
+      c->no_indels = 0;
++     c->approx_threshold_n = -1;
+ }
+ 
+ 
+@@ -1062,7 +1065,8 @@ int
+ snpcaller(long double *snp_pvalues,
+           const double *err_probs, const int num_err_probs,
+           const int *noncons_counts,
+-          const long long int bonf_factor, const double sig_level)
++          const long long int bonf_factor, const double sig_level,
++          const int approx_threshold_n)
+ {
+     double *probvec = NULL;
+     int i;
+@@ -1100,6 +1104,33 @@ snpcaller(long double *snp_pvalues,
+         goto free_and_exit;
+     }
+ 
++/* how to combine ifndef? */
++#ifndef HAVE_LIBGSL
++#ifndef HAVE_LIBGSLCBLAS
++     if (approx_threshold_n>0) {
++          LOG_FATAL("%s\n", "Can't use approximation. It was disabled during compile time");
++          exit(1);
++     }
++#endif
++#endif
++
++/* how to combine ifdef? */
++#ifdef HAVE_LIBGSL
++     #ifdef HAVE_LIBGSLCBLAS
++     /* Only approximate if sufficient data available */
++     if (approx_threshold_n > 0 && num_err_probs > approx_threshold_n) {
++          long double mu = 0;
++          for (int i = 0; i < num_err_probs; ++i) {
++               mu += err_probs[i];
++          }
++          const long double poibin_approximation = 1 - gsl_cdf_poisson_P(max_noncons_count - 1, mu);
++          if (poibin_approximation * (double)bonf_factor > sig_level) {
++               goto free_and_exit;
++          }
++     }
++     #endif
++#endif
++
+     probvec = poissbin(&pvalue, err_probs, num_err_probs,
+                        max_noncons_count, bonf_factor, sig_level);
+ 
+@@ -1120,7 +1151,6 @@ snpcaller(long double *snp_pvalues,
+         goto free_and_exit;
+     }
+ 
+-
+     /* report p-value for each non-consensus base
+      */
+     for (i=0; i<NUM_NONCONS_BASES; i++) {
+diff --git a/src/lofreq/snpcaller.h b/src/lofreq/snpcaller.h
+index 117505c..6822044 100644
+--- a/src/lofreq/snpcaller.h
++++ b/src/lofreq/snpcaller.h
+@@ -59,6 +59,7 @@ typedef struct {
+      int only_indels; 
+      int no_indels; 
+ 
++     int approx_threshold_n; /* when to use fast poisson binomial approximation for early exit */
+ } varcall_conf_t;
+ 
+ 
+@@ -97,7 +98,8 @@ extern int
+ snpcaller(long double *snp_pvalues, const double *err_probs,
+           const int num_err_probs, const int *noncons_counts,
+           const long long int bonf_factor,
+-          const double sig_level);
++          const double sig_level,
++          const int approx_treshold_n);
+ 
+ 
+ #endif
+diff --git a/src/scripts/lofreq2_call_pparallel.py b/src/scripts/lofreq2_call_pparallel.py
+index fc3e82c..64dd3c1 100755
+--- a/src/scripts/lofreq2_call_pparallel.py
++++ b/src/scripts/lofreq2_call_pparallel.py
+@@ -166,16 +166,23 @@ def concat_vcf_files(vcf_files, vcf_out, source=None):
+     """
+ 
+     assert not os.path.exists(vcf_out)
+-
+-    cmd = ['lofreq', 'vcfset', '-a', 'concat', '-o', vcf_out, '-1']
++    #I didn't address the FIXME issue noted above but another bug was fixed here.
++    #This now uses bcftools to overcome systematic failures of merging with certain data sets due to multi-allelic variants
++    cmd = ['bcftools', 'concat', '-a', '-O', 'z', '-o', vcf_out]
+     cmd.extend(vcf_files)
++    idx = ['bcftools','index','-t', vcf_out]
+     try:
+         subprocess.check_call(cmd)
+     except subprocess.CalledProcessError as e:
+         LOG.fatal("The following command failed with return code %d: %s" % (
+             e.returncode, ' '.join(cmd)))
+         sys.exit(1)
+-
++    try:
++        subprocess.check_call(idx)
++    except subprocess.CalledProcessError as e:
++        LOG.fatal("The following command failed with return code %d: %s" % (
++            e.returncode, ' '.join(cmd)))
++        sys.exit(1)
+ 
+ def sq_list_from_bam_samtools(bam):
+     """Extract SQs listed in BAM head using samtools
diff --git a/recipes/lofreq/build.sh b/recipes/lofreq/build.sh
index d349a75b80adb..8c72001e8eb35 100644
--- a/recipes/lofreq/build.sh
+++ b/recipes/lofreq/build.sh
@@ -1,6 +1,22 @@
 #!/bin/bash
 set -eu -o pipefail
 
-./configure --with-htslib=system --prefix=${PREFIX}
-make -j ${CPU_COUNT}
+export M4="${BUILD_PREFIX}/bin/m4"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
+
+if [[ "$(uname)" == Darwin ]]; then
+	export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+fi
+
+autoreconf -if
+./configure --with-htslib=system --prefix="${PREFIX}" \
+	CC="${CC}" CFLAGS="${CFLAGS}" \
+	LDFLAGS="${LDFLAGS}" \
+	CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" \
+	PYTHON="${PYTHON}"
+
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/lofreq/build_failure.osx-64.yaml b/recipes/lofreq/build_failure.osx-64.yaml
deleted file mode 100644
index f9584cf07d81e..0000000000000
--- a/recipes/lofreq/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: 4cf287f5a7c455a055c0d13140b029f5521f83c577150eb646297dd597f8e2c7  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: test failure
-log: |-
-  running install_egg_info
-  Writing $PREFIX/lib/python3.9/site-packages/LoFreq_Star-2.1.5-py3.9.egg-info
-  make[3]: Leaving directory '$SRC_DIR/src/tools'
-  make[2]: Nothing to be done for 'install-data-am'.
-  make[2]: Leaving directory '$SRC_DIR/src/tools'
-  make[1]: Leaving directory '$SRC_DIR/src/tools'
-  make[1]: Entering directory '$SRC_DIR'
-  make[2]: Entering directory '$SRC_DIR'
-  make[2]: Nothing to be done for 'install-exec-am'.
-  make[2]: Nothing to be done for 'install-data-am'.
-  make[2]: Leaving directory '$SRC_DIR'
-  make[1]: Leaving directory '$SRC_DIR'
-
-  Resource usage statistics from building lofreq:
-     Process count: 8
-     CPU time: Sys=0:00:00.3, User=0:00:00.6
-     Memory: 99.9M
-     Disk usage: 8.0K
-     Time elapsed: 0:00:14.7
-
-
-  Packaging lofreq
-  Packaging lofreq-2.1.5-py39h8037bd6_12
-
-
-  WARNING: Importing conda-verify failed.  Please be sure to test your packages.  conda install conda-verify to make this message go away.
-  compiling .pyc files...
-  number of files: 10
-     INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']'
-     INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']'
-     INFO: sysroot: '/opt/X11/' files: '[]'
-     INFO (lofreq,bin/lofreq): Needed DSO lib/libhts.3.dylib found in bioconda/osx-64::htslib==1.20=hec81eee_1
-     INFO (lofreq,bin/lofreq): Needed DSO lib/libz.1.dylib found in conda-forge/osx-64::libzlib==1.2.13=h87427d6_6
-     INFO (lofreq,bin/lofreq): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (lofreq): Interpreted package 'lofreq' is interpreted by 'python'
-  Fixing permissions
-  INFO :: Time taken to mark (prefix)
-          0 replacements in 0 files was 0.04 seconds
-  Files containing CONDA_PREFIX
-  -----------------------------
-  bin/lofreq2_indel_ovlp.py (text): Patching
-  bin/lofreq2_vcfplot.py (text): Patching
-  TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/lofreq-2.1.5-py39h8037bd6_12.tar.bz2
-  Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work' to '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work_moved_lofreq-2.1.5-py39h8037bd6_12_osx-64'
-  shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work_moved_lofreq-2.1.5-py39h8037bd6_12_osx-64)
-  Reloading output folder (local): ...working... done
-  Solving environment (_test_env): ...working... done
-
-  ## Package Plan ##
-
-    environment location: /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
-
-
-  The following NEW packages will be INSTALLED:
-
-      bzip2:           1.0.8-h10d778d_5          conda-forge
-      c-ares:          1.28.1-h10d778d_0         conda-forge
-      ca-certificates: 2024.6.2-h8857fd0_0       conda-forge
-      curl:            8.8.0-hea67d85_0          conda-forge
-      htslib:          1.20-hec81eee_1           bioconda
-      krb5:            1.21.2-hb884880_0         conda-forge
-      libcurl:         8.8.0-hf9fcc65_0          conda-forge
-      libcxx:          17.0.6-h88467a6_0         conda-forge
-      libdeflate:      1.20-h49d49c5_0           conda-forge
-      libedit:         3.1.20191231-h0678c8f_2   conda-forge
-      libev:           4.33-h10d778d_2           conda-forge
-      libffi:          3.4.2-h0d85af4_5          conda-forge
-      libnghttp2:      1.58.0-h64cf6d3_1         conda-forge
-      libsqlite:       3.46.0-h1b8f9f3_0         conda-forge
-      libssh2:         1.11.0-hd019ec5_0         conda-forge
-      libzlib:         1.3.1-h87427d6_1          conda-forge
-      lofreq:          2.1.5-py39h8037bd6_12     local
-      ncurses:         6.5-h5846eda_0            conda-forge
-      openssl:         3.3.1-h87427d6_0          conda-forge
-      python:          3.9.19-h7a9c478_0_cpython conda-forge
-      python_abi:      3.9-4_cp39                conda-forge
-      readline:        8.2-h9e318b2_1            conda-forge
-      samtools:        1.5-1                     bioconda
-      tk:              8.6.13-h1abcd95_1         conda-forge
-      tzdata:          2024a-h0c530f3_0          conda-forge
-      xz:              5.2.6-h775f41a_0          conda-forge
-      zlib:            1.3.1-h87427d6_1          conda-forge
-      zstd:            1.5.6-h915ae27_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-   lofreq version
-   samtools --help
-  dyld[51805]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
-    Referenced from: <8AD915FB-8A79-34FD-9167-D77089463421> /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/samtools
-    Reason: tried: '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file, not in dyld cache)
-  /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/test_tmp/run_test.sh: line 8: 51805 Abort trap: 6           samtools --help
-  WARNING: Tests failed for lofreq-2.1.5-py39h8037bd6_12.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
-  TESTS FAILED: lofreq-2.1.5-py39h8037bd6_12.tar.bz2
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/test_tmp
-  version: 2.1.5
-  commit: unknown
-  build-date: Jun 11 2024
-# Last 100 lines of the build log.
diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml
index 4dc0e346faf57..0d1ccfe2d7006 100644
--- a/recipes/lofreq/meta.yaml
+++ b/recipes/lofreq/meta.yaml
@@ -1,15 +1,17 @@
-{% set version="2.1.5" %}
+{% set version = "2.1.5" %}
 
 package:
   name: lofreq
   version: {{ version }}
 
 source:
-  url: https://raw.githubusercontent.com/CSB5/lofreq/v{{ version }}/dist/lofreq_star-{{ version }}.tar.gz
-  sha256: 43028af07faa23c7ec0e167855492ae7bd31c4e7f8158114e51ec12aba5fd184
+  url: https://github.com/CSB5/lofreq/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: da85ec4baca21e20a55b5f9ee491cdda2986d0dc672177007a2c70ca1d804fe7
+  patches:
+    - 0001-patches
 
 build:
-  number: 12
+  number: 13
   run_exports:
     - {{ pin_subpackage('lofreq', max_pin='x') }}
 
@@ -17,13 +19,20 @@ requirements:
   build:
     - make
     - {{ compiler('c') }}
+    - autoconf
+    - automake
+    - libtool
   host:
     - python
+    - setuptools  # [py >= 3.12]
     - htslib
+    - samtools
+    - gsl
     - zlib
   run:
     - python
     - samtools
+    - gsl
 
 test:
   commands:
@@ -31,12 +40,18 @@ test:
     - samtools --help
 
 about:
-  home: http://csb5.github.io/lofreq/
+  home: "https://csb5.github.io/lofreq"
   license: MIT
-  summary: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
+  license_family: MIT
+  license_file: LICENSE
+  summary: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data."
+  dev_url: "https://github.com/CSB5/lofreq"
+  doc_url: "https://csb5.github.io/lofreq"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - usegalaxy-eu:lofreq_call
+    - biotools:lofreq
diff --git a/recipes/macsyfinder/meta.yaml b/recipes/macsyfinder/meta.yaml
index e8304f673014b..e60f30f1d0927 100644
--- a/recipes/macsyfinder/meta.yaml
+++ b/recipes/macsyfinder/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   entry_points:
     - macsyfinder=macsypy.scripts.macsyfinder:main
@@ -27,16 +27,18 @@ requirements:
   host:
     - pip
     - python >=3.10
+    - setuptools
+
   run:
     - python >=3.10
     - colorlog
     - PyYAML >=5.1.1
     - packaging >=18.0
     - networkx >=2.4
-    - pandas >=1.1.5,<=1.5.1
+    - pandas >=1.1.5,<=2.2.3
     - colorama >=0.4.4
     - certifi
-    - hmmer >=3.1b2,<=3.3.2
+    - hmmer >=3.1b2,<=3.4
     - git >1.7.0
     - gitpython >=3.1.30 
 
diff --git a/recipes/marti/meta.yaml b/recipes/marti/meta.yaml
index e86203beedb7e..d9eafb176f1f1 100644
--- a/recipes/marti/meta.yaml
+++ b/recipes/marti/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "MARTi" %}
-{% set version = "0.9.16" %}
+{% set version = "0.9.18" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/richardmleggett/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 85b06a61df8860d17c6de5282a820a8bd1b66bbb3d1f2351dbf5b54522aa1cb6
+  sha256: 7983a39b9d597fbe40850f8d88dd8078aec064fa7053ff029119a5b85806232e
 
 build:
   noarch: generic
diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml
index 263f3b2f86013..6485c985ee7c8 100644
--- a/recipes/matchms/meta.yaml
+++ b/recipes/matchms/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 96d15fbc006c90ac306e91b9fc609255108c48536094d2a55502f6a2e65fbce8
 
 build:
-  number: 0
+  number: 1
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
@@ -19,26 +19,26 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.8,<3.12
+    - python >=3.9,<3.13
     - poetry-core
   run:
-    - deprecated
-    - lxml
-    - matplotlib-base
-    - networkx
-    - numba >=0.47
-    - numpy <1.25
+    - deprecated >=1.2.14
+    - lxml >=4.9.3,<5
+    - matplotlib-base >=3.7
+    - networkx >=3.0
+    - numba >=0.57.1,<0.60
+    - numpy >1.22,<1.27
     - pickydict >=0.4.0
     - pyteomics >=4.6
-    - python >=3.8,<3.12
-    - pyyaml
-    - rdkit >=2020.03.1
-    - requests
-    - scipy >=1.4.0,<1.11
+    - python >=3.9,<3.13
+    - pyyaml >=6.0.1
+    - rdkit >=2023.9.6
+    - requests >=2.31.0
+    - scipy >=1.11
     - sparsestack >=0.4.1
-    - tqdm
-    - pillow =9.5
-    - pandas
+    - tqdm >=4.65.0
+    - pillow !=9.4.0
+    - pandas >=2.0.3
     - pubchempy
 
 test:
diff --git a/recipes/mess/meta.yaml b/recipes/mess/meta.yaml
index 79e6e64a7263c..01c9ddfd0baad 100644
--- a/recipes/mess/meta.yaml
+++ b/recipes/mess/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: a0bb9d8dc81548cfad1cc45d43c82d41b28a399dd8f6bad4c5588a8201196f1a
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - mess=mess.__main__:main
@@ -21,19 +21,20 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.11
     - pip
+    - setuptools
 
   run:
-    - python >=3.10
-    - mamba >=1.5.8
+    - python >=3.11
+    - apptainer >=1.3.2
     - snakemake-minimal >=8.0.0
     - snaketool-utils >=0.0.5
     - attrmap >=0.0.7
     - pyyaml >=6.0.1
-    - pandas >=2.2.1
+    - pandas >=2.2.3
     - biopython >=1.83
-    - rich-click >=1.7.4
+    - rich-click >=1.8.3
 
 test:
   commands:
diff --git a/recipes/metabolabpy/meta.yaml b/recipes/metabolabpy/meta.yaml
index 1ebc73d558377..8b1c0343cd689 100644
--- a/recipes/metabolabpy/meta.yaml
+++ b/recipes/metabolabpy/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "metabolabpy" %}
-{% set version = "0.9.53" %}
-{% set sha256 = "33a3b653bc876908948578abb0354d146ab796cb234640a90a7ec1cadee19427" %}
+{% set version = "0.9.62" %}
+{% set sha256 = "2ec311c98aa7112cfee694c0d132dba4c7b33893bd950a8affc5acf11a561282" %}
 
 package:
   name: {{ name|lower }}
@@ -21,6 +21,7 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - numpy
diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml
index 69e44e55deb2e..62b9ce34f8b48 100644
--- a/recipes/metabolights-utils/meta.yaml
+++ b/recipes/metabolights-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.1.12" %}
+{% set version = "1.2.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: a9f482e77df79e1efa6c4884edd9b66f21ac7267cf2d8aa7bf9c018cc9c08788
+  sha256: 6698a1b4bdeda9aa0aea0329900f0fbbc8cae8e60f40fc316e5e5a03eec6ff20
 
 build:
   entry_points:
diff --git a/recipes/metagenome-atlas/meta.yaml b/recipes/metagenome-atlas/meta.yaml
index 0808fdc8b23ca..fe8a88e44c990 100644
--- a/recipes/metagenome-atlas/meta.yaml
+++ b/recipes/metagenome-atlas/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.18.2" %}
+{% set version = "2.19.0" %}
 
 package:
   name: metagenome-atlas
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/metagenome-atlas/atlas/archive/v{{ version }}.tar.gz
-  sha256: 33a3d4b0a479bb7ed561f316252c7b4e33d098c8445e0567520e55e1cf4cf1e0
+  sha256: d0a97c24be4e9b957003c99ba1807c971680fe2dccb29b586793de3cf3225f17
 
 build:
   number: 0
diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml
index eae9441d91acc..313c062578cfc 100644
--- a/recipes/mgnify-pipelines-toolkit/meta.yaml
+++ b/recipes/mgnify-pipelines-toolkit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mgnify-pipelines-toolkit" %}
-{% set version = "0.1.7" %}
+{% set version = "0.1.8" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz
-  sha256: 506eb725d226ff33ceaf8001502a0ab97bcaf41ac84ce011f98a2ccb892389ed
+  sha256: 57c299db9d80ab66c343d53a12382871eb166cf5e55470197ff4447fb7f93e78
 
 build:
   entry_points:
diff --git a/recipes/mikrokondo-tools/meta.yaml b/recipes/mikrokondo-tools/meta.yaml
new file mode 100644
index 0000000000000..1c96c8b6e9a71
--- /dev/null
+++ b/recipes/mikrokondo-tools/meta.yaml
@@ -0,0 +1,50 @@
+{% set name = "mikrokondo-tools" %}
+{% set version = "0.0.1rc0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://files.pythonhosted.org/packages/source/{{ name[0] }}/{{ name }}/mikrokondo_tools-{{ version }}.tar.gz
+  sha256: 97a6805c4de8acf568ea1be22a91b442a7c780f66d54520e1c9c8af9ef08d7ef
+
+build:
+  entry_points:
+    - mikrokondo-tools = mikrokondo_tools.cli:safe_entry_point
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.8
+    - hatchling
+    - pip
+  run:
+    - python >=3.8
+    - click
+    - requests
+    - jsonschema
+
+test:
+  imports:
+    - mikrokondo_tools
+  commands:
+    - pip check
+    - mikrokondo-tools --help
+  requires:
+    - pip
+
+about:
+  home: https://pypi.org/project/mikrokondo-tools
+  summary: A collection of utilities to make using the mikrokondo pipeline easier
+  dev_url: https://github.com/DOED-DAAD/mikrokondo-tools
+  license: Apache-2.0
+  license_file: LICENSE.txt
+
+extra:
+  recipe-maintainers:
+    - mattheww95
diff --git a/recipes/mkdesigner/meta.yaml b/recipes/mkdesigner/meta.yaml
index 7c89662a1d4a4..92a931f5b02ac 100644
--- a/recipes/mkdesigner/meta.yaml
+++ b/recipes/mkdesigner/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mkdesigner" %}
-{% set version = "0.4.4" %}
+{% set version = "0.5.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mkdesigner-{{ version }}.tar.gz
-  sha256: 29513140681b1f667764081bf981c1a548be3cf877bab4ffe551df96b1efbd9d
+  sha256: 532609a307abcabe2a090ea64a73d29092fafcd543d62d0d10fbadcee0ba9df5
 
 build:
   entry_points:
@@ -18,12 +18,13 @@ build:
   script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
   run_exports:
-    - {{ pin_subpackage('mkdesigner', max_pin="x") }}
+    - {{ pin_subpackage('mkdesigner', max_pin="x.x") }}
 
 requirements:
   host:
     - python >=3.8,<4.0
     - pip
+    - setuptools
   run:
     - python >=3.8,<4.0
     - pandas >=2.0.2,<3.0.0
@@ -34,6 +35,7 @@ requirements:
     - samtools >=1.6,<2.0
     - bcftools >=1.5,<2.0
     - matplotlib-base
+    - timeout-decorator
 
 test:
   imports:
@@ -44,11 +46,12 @@ test:
     - mkselect --help
 
 about:
-  home: https://github.com/KChigira/mkdesigner/
+  home: https://github.com/KChigira/mkdesigner
   summary: Genome-wide design of markers for PCR-based genotyping from NGS data.
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/KChigira/mkdesigner
 
 extra:
   recipe-maintainers:
diff --git a/recipes/mofapy2/meta.yaml b/recipes/mofapy2/meta.yaml
index 0b73846286177..22cf63bf5a500 100644
--- a/recipes/mofapy2/meta.yaml
+++ b/recipes/mofapy2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mofapy2" %}
-{% set version = "0.7.1" %}
+{% set version = "0.7.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 937c385e07cebcc20039cff4782b7f7d6ebb7b576c4f5a12f5e74364dcec16c3
+  sha256: 3bd7a2a7529ea7a9a91b22393079141b6e5ba5fa9c0895cdf6ff002dc26229f9
 build:
   noarch: python
   number: 0
diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml
index af3102cc3571f..4aebeeddd48cc 100644
--- a/recipes/ms2deepscore/meta.yaml
+++ b/recipes/ms2deepscore/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2deepscore" %}
-{% set version = "2.1.0" %}
-{% set sha256 = "ba844b923a6e1fb61c8dc24c8ea507ed5e502a81e8f675710ba76574498e5c9c" %}
+{% set version = "2.2.0" %}
+{% set sha256 = "c4f6458b88cf8ea95e4ec4b7b7872d0f4dc9c9f7e8c5538c8ff2e59c78b8bb15" %}
 
 package:
   name: {{ name|lower }}
@@ -21,6 +21,7 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - matchms >=0.18.0
diff --git a/recipes/msweep/meta.yaml b/recipes/msweep/meta.yaml
index c3f6dfbac8a1b..64708742989df 100644
--- a/recipes/msweep/meta.yaml
+++ b/recipes/msweep/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "mSWEEP" %}
-{% set version = "2.2.0" %}
-{% set sha256 = "9f2cbaaa877466a59171a4e74fe26d462657b62ae0e3b464672e44490a6f3d73" %}
+{% set version = "2.2.1" %}
+{% set sha256 = "16928507cdd62643b1e4d112fbc5757ef27c9d1f42fadfdd5c947894b2614382" %}
 {% set user = "PROBIC" %}
 
 package:
diff --git a/recipes/mtgrasp/meta.yaml b/recipes/mtgrasp/meta.yaml
index 5f957b450f1ba..bf9dc5d98802b 100644
--- a/recipes/mtgrasp/meta.yaml
+++ b/recipes/mtgrasp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.1.6" %}
+{% set version = "1.1.8" %}
 {% set name = "mtGrasp" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/bcgsc/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 07c558d607df8d250e181439f08a4d13e2930afc566a060ea5b11b59e18c721a 
+  sha256: e48ac50c69f607d75362c860cb7e1ded8456a4d7d1e603bd93d32b07e738cafa 
 
 build:
   number: 0
diff --git a/recipes/mutmap/meta.yaml b/recipes/mutmap/meta.yaml
index 4101005f5733b..e61f2ad291909 100644
--- a/recipes/mutmap/meta.yaml
+++ b/recipes/mutmap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "mutmap" %}
-{% set version = "2.3.6" %}
-{% set sha256 = "74db0af6b2c3c83767d13509a9098ebb5fbb7170455770b056916ba48876ddb7" %}
+{% set version = "2.3.8" %}
+{% set sha256 = "6a0883ceb4fc0bbd4b19ccc65bcbff349d89d2a8db8732e5ef2e0d8dade5b595" %}
 
 package:
   name: {{ name|lower }}
@@ -11,9 +11,12 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   noarch: python
   number: 0
+  entry_points:
+    - mutmap = mutmap.mutmap:main
+    - mutplot = mutmap.mutplot:main
   run_exports:
     - {{ pin_subpackage('mutmap', max_pin="x") }}
 
@@ -21,7 +24,7 @@ requirements:
   host:
     - python >=3.5
     - pip
-
+    - setuptools
   run:
     - python >=3.5
     - samtools >=1.7
@@ -33,7 +36,7 @@ requirements:
     - matplotlib-base
     - numpy
     - pandas
-    - seaborn
+    - seaborn-base
 
 test:
   commands:
@@ -41,10 +44,12 @@ test:
     - mutplot -h
 
 about:
-  home: https://github.com/YuSugihara/MutMap
-  summary: 'MutMap: pipeline to identify causative mutations responsible for a phenotype'
+  home: "https://github.com/YuSugihara/MutMap"
+  summary: 'MutMap: pipeline to identify causative mutations responsible for a phenotype.'
   license: 'GPL-3.0-or-later'
-  license_family: GPL
+  license_family: GPL3
+  license_file: LICENSE
+  dev_url: "https://github.com/YuSugihara/MutMap"
 
 extra:
   identifiers:
diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml
index a1aa81d780824..42bf68bb50358 100644
--- a/recipes/nanomotif/meta.yaml
+++ b/recipes/nanomotif/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "nanomotif" %}
-{% set version = "0.4.14" %}
+{% set version = "0.4.15" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz
-  sha256: 87dba57f2c2468c09605eddd9ead58bb0187d36dea67546df2ab52df94fdb75d
+  sha256: 5019e390130cc0dc63831e2658e41300e7b0fdc403b52bd3fdf35677afc5d879
 
 build:
   entry_points:
diff --git a/recipes/ncbi-stxtyper/meta.yaml b/recipes/ncbi-stxtyper/meta.yaml
index 22955929e7a18..df64553ebb334 100644
--- a/recipes/ncbi-stxtyper/meta.yaml
+++ b/recipes/ncbi-stxtyper/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.24" %}
-{% set sha256 = "54ddeb7ec1a052c141c32eea402c816f0515f47b7f0a5afeb054e410f9a4576f" %}
+{% set version = "1.0.25" %}
+{% set sha256 = "adc734340c6a10f1bfc34ca637197e93e1515d0231bd023b33ce4c07aab9578e" %}
 
 package:
   name: ncbi-stxtyper
diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml
index 0387300d88ae8..575258cfa9ae2 100644
--- a/recipes/neat/meta.yaml
+++ b/recipes/neat/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "NEAT" %}
-{% set version = "4.2.5" %}
+{% set version = "4.2.6" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz
-  sha256: ba3ef6233f236a89fd41af8a52a922e04b48c596d8573675c52da2682aaa4752
+  sha256: 04348e0539b6259ebd4a48a2c60325f04ee0b49323243ceedd675655ba9f94d6
   
 
 build:
diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml
index ee8272d6611b5..aca422e6b7be0 100644
--- a/recipes/nextclade/meta.yaml
+++ b/recipes/nextclade/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "nextclade" %}
-{% set version = "3.8.2" %}
+{% set version = "3.9.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,13 +7,13 @@ package:
 
 source:
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu   # [linux64]
-    sha256: 8366d5f7c8f131d8659aa2af1ab014d3ea0d429420dab90f90badbe827a532e6                                           # [linux64]
+    sha256: e42aaed0854ecdc5b8e8523c65e2388c57817a43e2725e0d98f959dd9c820111                                           # [linux64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu  # [aarch64]
-    sha256: 87fce29bbcfd84290073c0fc23f53ed7c7c459df35077bc11b360515e85917bb                                           # [aarch64]
+    sha256: f5a08e8bf33a9a6d68407a90fca6cbc77928027b247a1648155b51ab3fd7d680                                           # [aarch64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin        # [osx and x86_64]
-    sha256: 414a6c0057665f72f598d1d2051ded309cc7aa96c88468d7cf9322ed559c9013                                           # [osx and x86_64]
+    sha256: 5570cf7b59876bb62bd4444112e304cbe60c28ce5e5a3d168a62f401953b9149                                           # [osx and x86_64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin       # [osx and arm64]
-    sha256: a5fbd37742cce895bbe7a468f136f06e6ca56e8b44a65e7c52ff15d9a126aa00                                           # [osx and arm64]
+    sha256: e328400872efe15a761bc012f6c8144d7b50f0775bff95b77ce4ed816ed239c3                                           # [osx and arm64]
 
 build:
   number: 0
diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml
index 13b0e97045e44..1e70802b64441 100644
--- a/recipes/nf-test/meta.yaml
+++ b/recipes/nf-test/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.9.0" %}
+{% set version = "0.9.1" %}
 
 
 package:
@@ -13,7 +13,7 @@ build:
 
 source:
   url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz
-  sha256: 3e123ceba36b6e890cb12ad4e98792bf4dd2d7e55c36a549b28708df13df0dc7
+  sha256: 363981e9b2fd8faa78096795594f6af9a01ef9d807ea5c14359600466e35a7c3
 
 requirements:
   host:
diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml
index bd744ba3f9fc8..9ab8356346ac4 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.12" %}
-{% set sha256 = "eb979f31a9291c8285d0ec335102455e8ad0210f59ffddf8074b1fabf76061a3" %}
+{% set version = "2.11.21" %}
+{% set sha256 = "e9a479ada8d64d8c425ebeb9ad217f6a41583ae7a41e4ee1df52851cd71d2d8a" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/odgi/build.sh b/recipes/odgi/build.sh
index cd4b51ac50228..8d97950684e85 100644
--- a/recipes/odgi/build.sh
+++ b/recipes/odgi/build.sh
@@ -1,20 +1,25 @@
 #!/bin/bash
-export LIBRARY_PATH=${PREFIX}/lib
-export LD_LIBRARY_PATH=${PREFIX}/lib
-export CPATH=${PREFIX}/include
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${PREFIX}/include
-export CPP_INCLUDE_PATH=${PREFIX}/include
-export CXX_INCLUDE_PATH=${PREFIX}/include
-#cmake -H. -Bbuild -DPYTHON_EXECUTABLE:FILEPATH=$PYTHON -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast -Og'
-cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast'
-cmake --build build
+
 mkdir -p $PREFIX/bin
-mv bin/* $PREFIX/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Generic \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \
+	"${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
+
 PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'`
-mkdir -p $PREFIX/lib/python$PYVER/site-packages
-cp lib/*cpython* $PREFIX/lib/python$PYVER/site-packages
-cp lib/* $PREFIX/lib
-#set -x
-#python -c "import sys; sys.path.append('./lib'); import odgi_ffi"
-#python -c "import sys; sys.path.append('./lib'); import odgi"
+mkdir -p "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/*cpython* "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/* "${PREFIX}/lib"
diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml
index f75494a207e1f..4de1264118239 100644
--- a/recipes/odgi/meta.yaml
+++ b/recipes/odgi/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "odgi" %}
-{% set version = "0.8.6" %}
+{% set version = "0.9.0" %}
 
 package:
   name: "{{ name }}"
@@ -7,32 +7,31 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: a6db190b782608082b14b42c660389aa18010791de1e2d07e29f7f61d8787754
-  patches:
-    - patch
+  sha256: 73b181c371e619b5e3e5ee87649cb8de82b054e492dcd128d93cec42be062f2f
 
 build:
-  skip: True  # [osx or py27]
-  number: 2
+  skip: True  # [osx]
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
     - cmake
     - make
   host:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - zlib
-    - python
     - jemalloc
+    - python
     - pybind11
   run:
     - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - python
+    - jemalloc
     - pybind11
 
 test:
@@ -40,11 +39,19 @@ test:
     - odgi test
 
 about:
-  home: https://github.com/pangenome/odgi
+  home: "https://github.com/pangenome/odgi"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: An optimized dynamic genome/graph implementation
+  summary: "An optimized dynamic genome/graph implementation."
+  dev_url: "https://github.com/pangenome/odgi"
+  doc_url: "https://github.com/pangenome/odgi/blob/v{{ version }}/README.md"
 
 extra:
   recipe-maintainers:
     - AndreaGuarracino
+  identifiers:
+    - doi:10.1093/bioinformatics/btac308
+    - biotools:odgi
+    - usegalaxy-eu:odgi_viz
+    - usegalaxy-eu:odgi_build
diff --git a/recipes/odgi/patch b/recipes/odgi/patch
deleted file mode 100644
index f5e417a8ecd37..0000000000000
--- a/recipes/odgi/patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/pythonmodule.cpp b/src/pythonmodule.cpp
-index 6a7942b..e38b12b 100644
---- a/src/pythonmodule.cpp
-+++ b/src/pythonmodule.cpp
-@@ -5,6 +5,7 @@
- #include <pybind11/pybind11.h>
- #include <pybind11/functional.h>
- #include <pybind11/iostream.h>
-+#include <pybind11/stl.h>
- 
- namespace py = pybind11;
- 
diff --git a/recipes/panacus/meta.yaml b/recipes/panacus/meta.yaml
index af5bddd58cb9b..fa4b81e48bfac 100644
--- a/recipes/panacus/meta.yaml
+++ b/recipes/panacus/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "panacus" %}
-{% set version = "0.2.4" %}
+{% set version = "0.2.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/marschall-lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: e4709c5e3e4b5c445789406a0ebf06a2052e24bc5fcc3b540cacf8064c2ab478
+  sha256: 7b4e4aee52528c569ad663d0fcd00bd42f221f29f93f0768f18c2ac2d3f0d769
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml
index fa818eea373d8..6cf82d11d8f79 100644
--- a/recipes/pcaone/meta.yaml
+++ b/recipes/pcaone/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.4.7" %}
-{% set sha256 = "b077472ecaefc067d5aa7990453c5e46f09bdd5e07a391eca1077c9c3bc1ed76" %}
+{% set version = "0.4.8" %}
+{% set sha256 = "35c9c02d51db0d100e71cabf1d509ac3c70816b3a83c7a5313d43edf3e18cd55" %}
 
 
 package:
diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml
index dfba7f191c929..dde0c225012c5 100644
--- a/recipes/peaks2utr/meta.yaml
+++ b/recipes/peaks2utr/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "peaks2utr" %}
-{% set version = "1.3.3" %}
+{% set version = "1.4.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz
-  sha256: 5fab611d8039a210936f172ccf6fb90989c91e53fb8ea8b18026cbce8a35d9b7
+  sha256: e9fe8ead2e8f778d48697e9afd6f48cbb1398613d7083427b26085210598ce1d
 
 build:
   number: 0
diff --git a/recipes/pegas/meta.yaml b/recipes/pegas/meta.yaml
new file mode 100644
index 0000000000000..57b42671e6020
--- /dev/null
+++ b/recipes/pegas/meta.yaml
@@ -0,0 +1,52 @@
+{% set name = "pegas" %}
+{% set version = "0.2.13" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/liviurotiul/PeGAS/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 2c028caa90bb8825e1c64f2ca5bd5e80f82f6db1cb5c4609bed86157c954c1f8
+
+build:
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+requirements:
+  build:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - plotly >=5.0.0
+    - pandas >=1.3.5
+    - tqdm >=4.66.5
+    - matplotlib-base >=3.9.2
+    - networkx >=3.2
+    - snakemake-minimal >=7.32.4
+    - beautifulsoup4 >=4.12.3
+
+test:
+  commands:
+    - {{ name }} --help
+
+about:
+  home: https://github.com/liviurotiul/PeGAS
+  license: GPL-2.0-or-later
+  license_family: GPL
+  license_file: LICENSE
+  summary: "PeGAS is a Snakemake pipeline for genome analysis"
+  description: |
+    PeGAS is a Snakemake pipeline for genome analysis. It is designed to be
+    lightweight, easy to install, and easy to use.
+  doc_url: https://github.com/liviurotiul/PeGAS#readme
+  dev_url: https://github.com/liviurotiul/PeGAS/issues
+
+extra:
+  recipe-maintainers:
+    - liviurotiul
diff --git a/recipes/perl-excel-writer-xlsx/meta.yaml b/recipes/perl-excel-writer-xlsx/meta.yaml
index 48eb53c2c4999..39cfbc00cf29c 100644
--- a/recipes/perl-excel-writer-xlsx/meta.yaml
+++ b/recipes/perl-excel-writer-xlsx/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "perl-excel-writer-xlsx" %}
-{% set version = "1.13" %}
-{% set sha256 = "3d60b14e40cd6d93b8e5b40c1bf814122301107fe10e7e6b4120ed3fe87009c9" %}
+{% set version = "1.14" %}
+{% set sha256 = "ce9e2c24756ee0bfbc241c66fca62ac4c9e06a1fd0da7fffff8ccb322cbfb688" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.13.tar.gz
+  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.14.tar.gz
   sha256: {{ sha256 }}
 
 build:
diff --git a/recipes/pggb/meta.yaml b/recipes/pggb/meta.yaml
index 5b0a82197d30a..6497a8b080682 100644
--- a/recipes/pggb/meta.yaml
+++ b/recipes/pggb/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pggb" %}
-{% set version = "0.6.0" %}
+{% set version = "0.7.2" %}
 
 package:
   name: "{{ name }}"
@@ -7,30 +7,32 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: e201410e5b7ca7c598267797a7fa30b065a1b2b76ee5c309341a93fc489704f3
+  sha256: a687d5268b77d6bbbdb026d379975eed2afff148d7d73697a8421ca39b3ddbe9
 
 build:
-  noarch: generic
+  number: 0
+  skip: true # [osx]
   run_exports:
   - {{ pin_subpackage(name, max_pin='x.x') }}
-  number: 1
 
 requirements:
   run:
+    - wfmash ==0.14.0
+    - seqwish ==0.7.11
+    - smoothxg ==0.8.0
+    - odgi ==0.9.0
+    - gfaffix ==0.1.5b
+    - vg ==1.59.0
+    - vcfbub ==0.1.1
+    - vcflib ==1.0.10
+    - multiqc ==1.22
+    - python-igraph ==0.11.5
     - bc
     - tabix
-    - gfaffix ==0.1.5b
     - gsl 2.7.0 
-    - multiqc ==1.19
-    - odgi ==0.8.6
     - pigz
     - bcftools
-    - seqwish ==0.7.10
-    - smoothxg ==0.7.4
     - time
-    - vg 1.59.0
-    - wfmash ==0.13.0
-    - python-igraph ==0.10.4
 
 test:
   commands:
@@ -40,8 +42,10 @@ about:
   home: https://github.com/pangenome/pggb
   license: MIT
   license_file: LICENSE
-  summary: This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model).
+  summary: PanGenome Graph Building pipeline renders
 
 extra:
   recipe-maintainers:
     - AndreaGuarracino
+  skip-lints:
+    - should_be_noarch_generic
diff --git a/recipes/pgscatalog-utils/meta.yaml b/recipes/pgscatalog-utils/meta.yaml
index 9f2ccfa52bfaf..d2ad494269d8b 100644
--- a/recipes/pgscatalog-utils/meta.yaml
+++ b/recipes/pgscatalog-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pgscatalog-utils" %}
-{% set version = "1.4.1" %}
+{% set version = "1.4.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pgscatalog_utils-{{ version }}.tar.gz
-  sha256: e54e67f9a372e91a7cc640528c66a9989258bc5ae61e7d6972a5b8ef4e1aa2da
+  sha256: a6393687b1b38a1926f999434c6c459f03a4e625ca6a66075b55b82ce1cc186b
 
 build:
   noarch: python
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('pgscatalog-utils', max_pin='x.x') }}  
 
@@ -24,7 +24,7 @@ requirements:
   run:
     - python >=3.10.0,<4.0.0
     - pgscatalog.calc >=0.3.0,<0.4.0
-    - pgscatalog.core >=0.3.1,<0.4.0
+    - pgscatalog.core >=0.3.2,<0.4.0
     - pgscatalog.match >=0.3.3,<0.4.0
 
 test:
diff --git a/recipes/pgscatalog.core/meta.yaml b/recipes/pgscatalog.core/meta.yaml
index 5d51c105d3fcc..9db0cfa331250 100644
--- a/recipes/pgscatalog.core/meta.yaml
+++ b/recipes/pgscatalog.core/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pgscatalog.core" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pgscatalog_core-{{ version }}.tar.gz
-  sha256: 612cc10afc4bea0dc5edfc6b279fc92b76e6833a9152e5bd63a7f98da4a125ad
+  sha256: a91d1d20692af7473ca55a3a40c96b43cb65890fe3f1516a394e52c0fa515f34
 
 build:
   entry_points:
diff --git a/recipes/phanotate/meta.yaml b/recipes/phanotate/meta.yaml
index 590f533b90944..ebbce406e405e 100644
--- a/recipes/phanotate/meta.yaml
+++ b/recipes/phanotate/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "phanotate" %}
-{% set version = "1.6.5" %}
+{% set version = "1.6.6" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: "4be12306eeace16d018538499299b1e01f3fc5a904af5836ed0172eacdda3483"
+  sha256: "ef33ec3886d9934d43e5747afc316c4229800cfce60a009fa645ff307b96e162"
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 36]
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   run_exports:
diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml
index a000cd11dea91..945e20339b3fb 100644
--- a/recipes/phyloacc/meta.yaml
+++ b/recipes/phyloacc/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "PhyloAcc" %}
-{% set version = "2.4.1" %}
-{% set sha256 = "919203dc541c172f9e835b0568f6abd49999a24734957fec020b01161479282c" %}
+{% set version = "2.4.2" %}
+{% set sha256 = "effa443400fa1ebfa43de1daf551c8344f883bcf8d048a11e64fca64243a93fe" %}
 
 package:
   name: {{ name|lower }}
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 0
   skip: True  # [py < 311]
   run_exports:
     - {{ pin_subpackage('phyloacc', max_pin="x") }}
diff --git a/recipes/piawka/meta.yaml b/recipes/piawka/meta.yaml
index d95c3026687f4..873fd2896a466 100644
--- a/recipes/piawka/meta.yaml
+++ b/recipes/piawka/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "piawka" %}
-{% set version = "0.8.5" %}
+{% set version = "0.8.6" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/novikovalab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 50384263a2ad8cfd17e67092820e2636bef8f84619a59cd5986c3631cb450ecd
+  sha256: 5da0029ef43fbe159052e5523bcd7db69a4566bf8268fcd2db44d91521e028f6
 
 build:
   noarch: generic
diff --git a/recipes/pixelator/meta.yaml b/recipes/pixelator/meta.yaml
index 72c495e3f1b6a..f939562085a86 100644
--- a/recipes/pixelator/meta.yaml
+++ b/recipes/pixelator/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pixelator" %}
 {% set pypi_name = "pixelgen-pixelator" %}
-{% set version = "0.18.2" %}
+{% set version = "0.18.3" %}
 
 package:
   name: {{ name|lower }}
@@ -8,7 +8,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ pypi_name[0] }}/{{ pypi_name }}/pixelgen_pixelator-{{ version }}.tar.gz
-  sha256: b2ae77b1118f804c47cb71e0af3b64d05657e670a9a0f24d79f57bacb38c2fcb
+  sha256: cc3ae8ef379b13c07fc1a8511f849b914791d6ecbf64055594a0026708b39708
 
 build:
   entry_points:
diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml
index 815d6fcdac78e..c397df4f393e8 100644
--- a/recipes/pneumo-typer/meta.yaml
+++ b/recipes/pneumo-typer/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "pneumo-typer" %}
-{% set version = "1.0.2" %}
+{% set version = "1.0.3" %}
 
-{% set sha256 = "755584efcb967c3afe260650af905123f81e192707ee8078ed9d1db22bbfad41" %}
+{% set sha256 = "2e9c4d071a5415281b4cafbdc86ad960e8c0805fa4469a350986109c6457d12e" %}
 
 package:
   name: "{{ name|lower }}"
@@ -12,7 +12,7 @@ source:
     sha256: {{ sha256 }}
     
 build:
-  number: 1
+  number: 0
   noarch: generic
   run_exports:
     - {{ pin_subpackage('pneumo-typer', max_pin="x") }}
@@ -22,9 +22,9 @@ requirements:
   
   run:
     - blast
-    - perl-gd
+    - perl-gd >=2.74
     - perl-gd-svg
-    - perl-svg
+    - perl-svg >=2.87
     - perl-bioperl-core
     - prodigal
     - blat
diff --git a/recipes/pybbi/meta.yaml b/recipes/pybbi/meta.yaml
index b7f67a6ef39f1..6bbaf82e9fbe0 100644
--- a/recipes/pybbi/meta.yaml
+++ b/recipes/pybbi/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybbi" %}
-{% set version = "0.4.0" %}
+{% set version = "0.4.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: "afafbc23f16f789344a454fce619af5556a67a2e11b7c36de8fc6f091e2478fc"
+  sha256: "6a193dcd0d4d4575c258d6cd5d2d7c5368a5cf58e939d8faae9f8fe192373a5c"
 
 build:
   number: 1
@@ -47,5 +47,7 @@ about:
   summary: "Python bindings to UCSC Big Binary (bigWig/bigBed) file library"
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - Nanguage
diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index beafd6b9e4426..07f43e97d3b13 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.188" %}
+{% set version = "1.2.205" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 7c0ecd9edbbd94b5aaddf7d412d42d5e24de9d705bbf70422175e9bae6a35bae
+  sha256: 79693b4ebc2b89703f6b2dcf1134b65840d3505b32a6c866009f276ce0da99de
 
 build:
   number: 0
diff --git a/recipes/pyfastani/meta.yaml b/recipes/pyfastani/meta.yaml
index d3da1db4f2b3b..6449236f384f7 100644
--- a/recipes/pyfastani/meta.yaml
+++ b/recipes/pyfastani/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pyfastani" %}
-{% set version = "0.5.1" %}
+{% set version = "0.6.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,12 +7,11 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: ad6c28303290a2389c29ed20db8266bbc4bf89a5b1bf64a7514d1bc9c6ba2d92
+  sha256: 255e890d3ee6bbd051bb94d71a5245703b254be1ff2b5dc6789d28b715ec5fa9
 
 build:
-  number: 1
-  skip: True  #[py2k]
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -20,15 +19,16 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - cmake >=3.20
+    - make
   host:
     - python
     - pip
     - cython
-    - setuptools
     - zlib
+    - scikit-build-core
   run:
     - python
-    - zlib
 
 test:
   imports:
@@ -39,10 +39,15 @@ test:
 about:
   home: https://github.com/althonos/pyfastani
   license: MIT
+  license_family: MIT
   license_file: COPYING
-  summary: Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation..
-  doc_url: https://pyfastani.readthedocs.org/
+  summary: "Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation."
+  doc_url: https://pyfastani.readthedocs.org
+  dev_url: https://github.com/althonos/pyfastani
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   recipe-maintainers:
     - althonos
diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml
new file mode 100644
index 0000000000000..adffe0a2b168d
--- /dev/null
+++ b/recipes/pyhmmsearch/meta.yaml
@@ -0,0 +1,46 @@
+{% set name = "pyhmmsearch" %}
+{% set version = "2024.10.20" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pyhmmsearch-{{ version }}.tar.gz
+  sha256: fc654467ab29758e43638ea61e2ec6ddc0332f377bd7ce0e334099a0103dfbf9
+
+build:
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  noarch: python
+  entry_points:
+    - pyhmmsearch=pyhmmsearch.pyhmmsearch:main
+    - reformat_pyhmmsearch=pyhmmsearch.reformat_pyhmmsearch:main
+    - serialize_hmm_models=pyhmmsearch.serialize_hmm_models:main
+  run_exports:
+    - {{ pin_subpackage("pyhmmsearch", max_pin=None) }}
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - pyhmmer >=0.10.12
+    - pandas >=2
+    - tqdm >=4
+
+test:
+  commands:
+    - pyhmmsearch --help
+    - reformat_pyhmmsearch --help
+    - serialize_hmm_models --help
+
+about:
+  home: "https://github.com/new-atlantis-labs/pyhmmsearch-stable"
+  summary: "Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer."
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: "https://github.com/new-atlantis-labs/pyhmmsearch-stable"
+  doc_url: "https://github.com/new-atlantis-labs/pyhmmsearch-stable/blob/main/README.md"
diff --git a/recipes/pykofamsearch/meta.yaml b/recipes/pykofamsearch/meta.yaml
new file mode 100644
index 0000000000000..2eae16bea7e77
--- /dev/null
+++ b/recipes/pykofamsearch/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "pykofamsearch" %}
+{% set version = "2024.10.20" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pykofamsearch-{{ version }}.tar.gz
+  sha256: f9455f343095327bab331a35010867d5d60f67b13bd5c2344d012e6801e48fad
+
+build:
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  noarch: python
+  entry_points:
+    - pykofamsearch=pykofamsearch.pykofamsearch:main
+    - reformat_enzymes=pykofamsearch.reformat_enzymes:main
+    - reformat_pykofamsearch=pykofamsearch.reformat_pykofamsearch:main
+    - serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
+    - subset_serialized_models=pykofamsearch.subset_serialized_models:main
+  run_exports:
+    - {{ pin_subpackage("pykofamsearch", max_pin=None) }}
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - pyhmmer >=0.10.12
+    - pandas >=2
+    - tqdm >=4
+
+test:
+  commands:
+    - pykofamsearch --help
+    - reformat_enzymes --help
+    - reformat_pykofamsearch --help
+    - serialize_kofam_models --help
+    - subset_serialized_models --help
+
+about:
+  home: "https://github.com/jolespin/pykofamsearch"
+  summary: "Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer."
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: "https://github.com/jolespin/pykofamsearch"
diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml
index 8a197411ebe35..3dbd07424f027 100644
--- a/recipes/pyteomics/meta.yaml
+++ b/recipes/pyteomics/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "4.7.4" %}
+{% set version = "4.7.5" %}
 
 package:
   name: pyteomics
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz
-  sha256: cd8a9b48ea3a3075bbbc3085880b5a4f76eb7359e3c71ee3948d9bb2aa48883b
+  sha256: 382aeaa8b921bdd2a7e5b4aa9fe46c6184bb43701205a845b4b861ee3e88f46a
 
 build:
   noarch: python
diff --git a/recipes/qtlseq/meta.yaml b/recipes/qtlseq/meta.yaml
index c652240449426..83056cb76fadc 100644
--- a/recipes/qtlseq/meta.yaml
+++ b/recipes/qtlseq/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "qtlseq" %}
-{% set version = "2.2.6" %}
-{% set sha256 = "dd21dc8a7c75e330d3333356a113373e342e298882511e15f7da801035957e4f" %}
+{% set version = "2.2.8" %}
+{% set sha256 = "fe4fd97a50a2240d60987f4c7dc67db2dee23654a5ec34bd08e30108a0ed1bdc" %}
 
 package:
   name: {{ name|lower }}
@@ -11,9 +11,12 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   noarch: python
   number: 0
+  entry_points:
+    - qtlseq = qtlseq.qtlseq:main
+    - qtlplot = qtlseq.qtlplot:main
   run_exports:
     - {{ pin_subpackage('qtlseq', max_pin="x") }}
 
@@ -21,6 +24,7 @@ requirements:
   host:
     - python >=3.5
     - pip
+    - setuptools
   run:
     - python >=3.5
     - samtools >=1.7
@@ -32,7 +36,7 @@ requirements:
     - matplotlib-base
     - numpy
     - pandas
-    - seaborn
+    - seaborn-base
 
 test:
   commands:
@@ -41,9 +45,10 @@ test:
 
 about:
   home: https://github.com/YuSugihara/QTL-seq
-  summary: 'QTL-seq: pipeline to identify causative mutations responsible for a phenotype'
+  summary: 'QTL-seq: pipeline to identify causative mutations responsible for a phenotype.'
   license: 'GPL-3.0-or-later'
-  license_family: GPL
+  license_family: GPL3
+  dev_url: https://github.com/YuSugihara/QTL-seq
 
 extra:
   identifiers:
diff --git a/recipes/r-chromvarmotifs/build.sh b/recipes/r-chromvarmotifs/build.sh
new file mode 100644
index 0000000000000..9df03d64c4e0e
--- /dev/null
+++ b/recipes/r-chromvarmotifs/build.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+# shellcheck disable=SC2086
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-chromvarmotifs/conda_build_config.yaml b/recipes/r-chromvarmotifs/conda_build_config.yaml
new file mode 100644
index 0000000000000..92f956ee470c1
--- /dev/null
+++ b/recipes/r-chromvarmotifs/conda_build_config.yaml
@@ -0,0 +1,4 @@
+r_base:
+  - 4.1
+  - 4.2
+  - 4.3
diff --git a/recipes/r-chromvarmotifs/meta.yaml b/recipes/r-chromvarmotifs/meta.yaml
new file mode 100644
index 0000000000000..53289b4a089f7
--- /dev/null
+++ b/recipes/r-chromvarmotifs/meta.yaml
@@ -0,0 +1,45 @@
+{% set version = "0.2.0" %}
+{% set github = "https://github.com/GreenleafLab/chromVARmotifs" %}
+{% set commit = "38bed559c1f4770b6c91c80bf3f8ea965da26076" %}
+
+package:
+  name: r-chromvarmotifs
+  version: "{{ version }}"
+
+source:
+  url: "{{ github }}/archive/{{ commit }}.zip"
+  sha256: 4e3bd3201bb4680d78e7786a6c85af06f935a3be8117a87ef03ba375926ebe74
+
+build:
+  noarch: generic
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  run_exports:
+    - {{ pin_subpackage("r-chromvarmotifs", max_pin="x.x") }}
+
+requirements:
+  host:
+    - r-base
+    - bioconductor-tfbstools
+  run:
+    - r-base
+    - bioconductor-tfbstools
+
+test:
+  commands:
+    - $R -e "library(chromVARmotifs)"
+
+about:
+  home: {{ github }}
+  license: MIT
+  license_family: MIT
+  license_file:
+    - {{ environ["PREFIX"] }}/lib/R/share/licenses/MIT
+    - LICENSE
+  summary: Stores several motifs as PWMatrixList objects for use in R with packages like motifmatchr and chromVAR.
+
+extra:
+  recipe-maintainers:
+    - mfansler
diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml
index 6efa5b0ac1291..c08984074b2f0 100644
--- a/recipes/r-grain/meta.yaml
+++ b/recipes/r-grain/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '1.4.4' %}
+{% set version = '1.4.5' %}
 
 package:
   name: r-grain
@@ -8,7 +8,7 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/gRain_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/gRain/gRain_{{ version }}.tar.gz
-  sha256: 4a94f9f6efad7e6c9304f67f8b60e378539e31ed1a45d425df21ce4b8f3a4eae
+  sha256: b31b46dab12ca071d67c480ec70106ef05afdc7142f68c0af5c8cff3384d900b
 
 build:
   number: 0
diff --git a/recipes/r-grbase/meta.yaml b/recipes/r-grbase/meta.yaml
index fd80555d344a1..d7d5dc795c461 100644
--- a/recipes/r-grbase/meta.yaml
+++ b/recipes/r-grbase/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '2.0.2' %}
+{% set version = '2.0.3' %}
 
 package:
   name: r-grbase
@@ -8,7 +8,7 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/gRbase_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/gRbase/gRbase_{{ version }}.tar.gz
-  sha256: 36720e49b82e360166386c9b3bf17838aeb6d9b921e7e01d48f8a115f9a02e97
+  sha256: 2ac60cbf683f1bebd3fbc50f3e71d76ff9e0b1daa441c397b0b7c43b326f1ba2
 
 build:
   number: 0
diff --git a/recipes/r-presto/conda_build_config.yaml b/recipes/r-presto/conda_build_config.yaml
new file mode 100644
index 0000000000000..92f956ee470c1
--- /dev/null
+++ b/recipes/r-presto/conda_build_config.yaml
@@ -0,0 +1,4 @@
+r_base:
+  - 4.1
+  - 4.2
+  - 4.3
diff --git a/recipes/r-presto/meta.yaml b/recipes/r-presto/meta.yaml
index 5cf1e0652e250..1f91ce9cadbf2 100644
--- a/recipes/r-presto/meta.yaml
+++ b/recipes/r-presto/meta.yaml
@@ -1,19 +1,23 @@
 {% set version = '1.0.0' %}
+{% set github = 'https://github.com/immunogenomics/presto' %}
+
 package:
   name: r-presto
   version: {{ version|replace("-", "_") }}
+  
 source:
-  url: https://github.com/immunogenomics/presto/archive/31dc97fed5e2e7fc323ae4af62f72181cc51d9a3.tar.gz
-  sha256: 720ef58aba219af03344e0ae0408fc48feda50e6b7f7f4af2251eb24ce1bfb88
+  url: {{ github }}/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 96e1b3a2fec84bbd0781d4d3235e33003cd4eb28944a433868ba446b956abcdb
+
 build:
-  script: $R CMD INSTALL --build .
-  run_exports:
-    - {{ pin_subpackage("r-presto", max_pin="x.x.x") }}
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
-# Suggests: knitr, rmarkdown, testthat, Seurat, SingleCellExperiment, SummarizedExperiment, broom, BiocStyle, DESeq2
+  run_exports:
+    - {{ pin_subpackage("r-presto", max_pin="x.x.x") }}
+  script: $R CMD INSTALL --build .
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -40,15 +44,22 @@ requirements:
     - r-rlang
     - r-tibble
     - r-tidyr
+
 test:
   commands:
     - $R -e "library('presto')"
+
 about:
-  home: https://github.com/immunogenomics/presto
+  home: {{ github }}
+  doc_url: https://immunogenomics.github.io/presto/
   license: GPL-3.0-only
+  license_family: GPL3
+  license_file:
+    - {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3
   summary: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces
     to dense and sparse matrices, as well as genomics analysis frameworks Seurat and
     SingleCellExperiment.
-  license_family: GPL3
-  license_file:
-    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+
+extra:
+  recipe-maintainers:
+    - mfansler
diff --git a/recipes/r-saccharis/LICENSE.md b/recipes/r-saccharis/LICENSE.md
new file mode 100644
index 0000000000000..175443ce88558
--- /dev/null
+++ b/recipes/r-saccharis/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
+
+_Version 3, 29 June 2007_  
+_Copyright © 2007 Free Software Foundation, Inc. &lt;<http://fsf.org/>&gt;_
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
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+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the “copyright” line and a pointer to
+where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+&lt;<http://www.gnu.org/licenses/>&gt;.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+&lt;<http://www.gnu.org/philosophy/why-not-lgpl.html>&gt;.
diff --git a/recipes/r-saccharis/build.sh b/recipes/r-saccharis/build.sh
new file mode 100644
index 0000000000000..6cf75266b7b4c
--- /dev/null
+++ b/recipes/r-saccharis/build.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+$R CMD INSTALL --build .
\ No newline at end of file
diff --git a/recipes/r-saccharis/conda_build_config.yaml b/recipes/r-saccharis/conda_build_config.yaml
new file mode 100644
index 0000000000000..57fea7b547a0d
--- /dev/null
+++ b/recipes/r-saccharis/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 4.3.*
\ No newline at end of file
diff --git a/recipes/r-saccharis/meta.yaml b/recipes/r-saccharis/meta.yaml
new file mode 100644
index 0000000000000..3a33ae82c1eed
--- /dev/null
+++ b/recipes/r-saccharis/meta.yaml
@@ -0,0 +1,62 @@
+{% set version = "1.0.5" %}
+  {% set name = "r-saccharis" %}
+  {% set build_number = 0%}
+  {% set filehash = "187B8244DD2357D7B1ED448AC72A5F172086CC823816A7149274A6AB469AF7C3"%}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url:
+    - 'https://github.com/saccharis/rsaccharis/releases/download/{{ version }}/rsaccharis_{{ version }}.tar.gz'
+  sha256: {{ filehash|lower}}
+
+build:
+  noarch: generic
+  number: {{ build_number }}
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  run_exports:
+    - {{ pin_subpackage("r-saccharis", max_pin="x.x") }}
+
+requirements:
+  host:
+    - r-base
+    - r-jsonlite
+    - r-ape
+    - r-stringr
+    - r-knitr
+    - r-dplyr
+    - r-magrittr
+    - r-rcolorbrewer
+    - r-ggnewscale
+    - r-ggplot2
+    - bioconductor-ggtree
+  run:
+    - r-base
+    - r-jsonlite
+    - r-ape
+    - r-stringr
+    - r-knitr
+    - r-dplyr
+    - r-magrittr
+    - r-rcolorbrewer
+    - r-ggnewscale
+    - r-ggplot2
+    - bioconductor-ggtree
+
+test:
+  commands:
+    - 'Rscript -e "library(rsaccharis)"'
+
+about:
+  home: 'https://github.com/saccharis/rsaccharis'
+  license: 'GPL-3.0-or-later'
+  license_family: GPL
+  summary: 'A rendering package for creating phylogenetic trees from SACCHARIS .json and .tree files, in the R statistical computing language.'
+  description: 'This package will use metadata .json and .tree files output from SACCHARIS v2 to generate annotated phylogenetic tree PDF files.
+    Highly customizable, as the formatting of the tree is done using ggplot2. Of course plotting functions can easily be manipulated as desired.
+    To use, call A_load_data() and B_plots_all() and follow prompts. Our default plots used for publication are domain_ECno_numeric.'
+  license_file: LICENSE.md
diff --git a/recipes/r-spacexr/meta.yaml b/recipes/r-spacexr/meta.yaml
index 241ba913d5238..2fa7bafc68543 100644
--- a/recipes/r-spacexr/meta.yaml
+++ b/recipes/r-spacexr/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: 7d980ecea377a0e2131a87c3ff2b66f512ac69ecc96c2e2b8c1dd4d4f02403f8
 
 build:
-  number: 0
+  number: 1
   noarch: generic  # Specify that the package is noarch
   run_exports: '{{ pin_compatible("r-spacexr", max_pin="x.x") }}'
   rpaths:
@@ -66,6 +66,7 @@ requirements:
     - r-scales
     - r-lifecycle
     - r-evaluate
+    - openssh
 test:
   commands:
     - $R -e "library(spacexr)"
diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml
index aabaddcf9f40e..1e6175440b972 100644
--- a/recipes/rbpbench/meta.yaml
+++ b/recipes/rbpbench/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "RBPBench" %}
-{% set version = "1.0" %}
-{% set sha256 = "04d94acb727cadf096adf7f023e629361fb6340ef47d47de8977a0d6b76f64aa" %}
+{% set version = "1.0.1" %}
+{% set sha256 = "ab36aaf9fe18500101cb82045220cd649436d4ae42e1c8311a85392482d294fb" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml
index 4ae4f2d4d6aa7..6f36f750e1005 100644
--- a/recipes/rmats/meta.yaml
+++ b/recipes/rmats/meta.yaml
@@ -10,7 +10,7 @@ source:
   url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz
 
 build:
-  number: 2
+  number: 3
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -26,14 +26,14 @@ requirements:
     - python
     - cython
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - libblas
     - liblapack
   run:
     - python
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - star >=2.5
 
@@ -50,4 +50,4 @@ about:
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
diff --git a/recipes/ropebwt3/meta.yaml b/recipes/ropebwt3/meta.yaml
index 8128c0239fb51..85d2f2305f02f 100644
--- a/recipes/ropebwt3/meta.yaml
+++ b/recipes/ropebwt3/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ropebwt3" %}
-{% set version = "3.7" %}
+{% set version = "3.8" %}
 
 package:
   name: {{ name }}
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/lh3/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 10a8f2974b5117a62bb490c231bd2539826cedea458798acd3273dc7b6baf9b8
+  sha256: 80564af84102cf9eb3d74502d2fdca8ffbba1ce9fcd207a5a40200bf48202f4e
 
 requirements:
   build:
diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml
index e6db3e56acfad..23f5ba01faa0d 100644
--- a/recipes/rosella/meta.yaml
+++ b/recipes/rosella/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.5.4" %}
+{% set version = "0.5.5" %}
 {% set name = "rosella" %}
-{% set hash = "6e398c335bf23ae55c1ea472d234c706fa7095769e87eb28f213c4950de08cb3" %}
+{% set hash = "9963ea2333e74b9c984c0b32aea4b4e22e1294f8ecd08ffb7db2d687cae97f05" %}
 
 package:
   name: rosella
diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml
index 063aa6d4133ec..da1b56e67a473 100644
--- a/recipes/rseqc/meta.yaml
+++ b/recipes/rseqc/meta.yaml
@@ -1,55 +1,53 @@
-{% set name = "RSeQC" %}
-{% set version = "5.0.3" %}
+{% set name = "rseqc" %}
+{% set version = "5.0.4" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 869f542e08f50c8874280d58e4f5565857b0aebac66a8eceef3f23016175061e
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rseqc-{{ version }}.tar.gz
+  sha256: b7f3996f3de0b0b0a09eec949281a8f3e665a20827fcb3cbbd7546b94574a088
 
 build:
-  number: 3
-  skip: True  # [py2k]
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv"
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 requirements:
-  build:
-    - {{ compiler('c') }}
   host:
     - pip
-    - python
-    - cython >=0.12
-    - nose
+    - python >=3.5
+    - setuptools
   run:
     - bx-python
     - numpy
     - pybigwig
     - pysam
-    - python
-    - r-base
-    - pandas
+    - python >=3.5
+    - logomaker
 
 test:
   imports:
     - qcmodule
     - qcmodule.SAM
+    - psyco_full
   commands:
     - read_distribution.py 2>&1 | grep Usage > /dev/null
     - geneBody_coverage.py 2>&1 | grep Usage > /dev/null
 
 about:
-  home: http://rseqc.sourceforge.net/
-  license: GNU General Public License v2 (GPLv2)
-  summary: 'RNA-seq QC Package'
+  home: "https://rseqc.sourceforge.net"
+  license: "GPL-2.0-or-later"
+  summary: 'QC package for RNA-seq data.'
   license_family: GPL2
+  license_file: LICENSE
+  dev_url: "https://rseqc.sourceforge.net"
+  doc_url: "https://rseqc.sourceforge.net/#usage-information"
 
 extra:
-  additional-platforms:
-    - linux-aarch64
   identifiers:
     - biotools:rseqc
     - doi:10.1093/bioinformatics/bts356
diff --git a/recipes/sainsc/meta.yaml b/recipes/sainsc/meta.yaml
index d426091bed58c..b6417121ec76a 100644
--- a/recipes/sainsc/meta.yaml
+++ b/recipes/sainsc/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "sainsc" %}
-{% set version = "0.1.1" %}
+{% set version = "0.2.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sainsc-{{ version }}.tar.gz
-  sha256: 43afd7d2c9f1b8b891893cfe730175d0e01d5443b7f17981a233109df4cbb228
+  sha256: af964871f73b31177cf1a31844b6c40323384e0bd3c97ab2520ecbec23036d72
 
 build:
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 2
-  skip: True  # [(osx and not arm64) or py<310]
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  skip: True  # [(osx and not arm64) or py < 310]
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -36,23 +36,21 @@ requirements:
     - polars >=1
     - scikit-image >=0.18
     - scipy >=1.9
-    - seaborn >=0.11
+    - seaborn-base >=0.11
+    - typing-extensions >=4
 
 test:
   imports:
     - sainsc
-  commands:
-    - pip check
-  requires:
-    - pip
 
 about:
   home: https://github.com/HiDiHlabs/sainsc
-  summary: Segmentation-free Analysis of In Situ Capture data
+  summary: "Segmentation-free Analysis of In Situ Capture data."
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  doc_url: https://sainsc.readthedocs.io/
+  doc_url: https://sainsc.readthedocs.io
+  dev_url: https://github.com/HiDiHlabs/sainsc
 
 extra:
   additional-platforms:
diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml
index 53a05b2658cd2..f9c03bb28ca14 100644
--- a/recipes/savana/meta.yaml
+++ b/recipes/savana/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "savana" %}
-{% set version = "1.2.2" %}
+{% set version = "1.2.3" %}
 
 package:
   name: "{{ name }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz"
-  sha256: c4a72c13d712930e8bc8e0865767c00708062edf4eec6f1bc951877c58f08380
+  sha256: 3d7b7258b59b7f8bc2704eed131df81db77931f790c86b7af19100554fa9d44f
 
 build:
   number: 0
@@ -22,6 +22,8 @@ build:
 requirements:
   build:
     - python >=3.9
+    - pip
+    - setuptools
   run:
     - python >=3.9
     - pybedtools >=0.9.0
diff --git a/recipes/sawfish/meta.yaml b/recipes/sawfish/meta.yaml
index e904065d7c71e..97818ecfc31b2 100644
--- a/recipes/sawfish/meta.yaml
+++ b/recipes/sawfish/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "sawfish" %}
-{% set version = "0.12.5" %}
+{% set version = "0.12.7" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/PacificBiosciences/sawfish/releases/download/v{{ version }}/sawfish-v{{ version }}-x86_64-unknown-linux-gnu.tar.gz
-  sha256: fefbeb104a6784bbe7a1cb39470054cf25136ce75540547b63e4fb74fa614c7e
+  sha256: 6af341da0452856da58e77f6e843275b9d6811114c222cef05f2e78add58bb4a
 
 build:
   number: 0
diff --git a/recipes/scoring-matrices/meta.yaml b/recipes/scoring-matrices/meta.yaml
index b97fea1eea695..7fb42273f3616 100644
--- a/recipes/scoring-matrices/meta.yaml
+++ b/recipes/scoring-matrices/meta.yaml
@@ -1,18 +1,17 @@
 {% set name = "scoring-matrices" %}
 {% set module = "scoring_matrices" %}
-{% set version = "0.2.2" %}
+{% set version = "0.3.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 2192df3f5f8ecd144071858cc287c958d2a842cdc8cc082c13755dfefe2f66b8
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ module }}-{{ version }}.tar.gz"
+  sha256: 0eba50087f65f752cb7ac3c20f58cbbae6650ed923c3c48070245b64bdebb3cb
 
 build:
-  number: 1
-  skip: True  # [py < 36]
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
@@ -20,12 +19,15 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+    - 'cmake >=3.20'
+    - make
   host:
-    - python
+    - 'python >=3.7'
     - pip
     - cython
+    - scikit-build-core
   run:
-    - python
+    - 'python >=3.7'
 
 test:
   imports:
diff --git a/recipes/sdeper/meta.yaml b/recipes/sdeper/meta.yaml
index 864ce86a9107a..bae38c70ea264 100755
--- a/recipes/sdeper/meta.yaml
+++ b/recipes/sdeper/meta.yaml
@@ -1,7 +1,7 @@
 # This is the recipe file to publish SDePER to Bioconda
 
 {% set name = "sdeper" %}
-{% set version = "1.6.2" %}
+{% set version = "1.6.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -9,7 +9,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 271371a6cdd717244c96ce7ba0c6e282f9cd85112048aac3a0ab40975724a1e4
+  sha256: 2b77042525519a1de5c07956e562fe2f0173e411a921826c4ab6b6ca1f5d6e10
 
 build:
   number: 0
diff --git a/recipes/seismic-rna/meta.yaml b/recipes/seismic-rna/meta.yaml
index 50b488e1e2409..4dd421e1aef29 100644
--- a/recipes/seismic-rna/meta.yaml
+++ b/recipes/seismic-rna/meta.yaml
@@ -2,7 +2,7 @@
 
 package:
   name: seismic-rna
-  version: 0.21.0
+  version: 0.21.1
 
 about:
   home: https://github.com/rouskinlab/seismic-rna
@@ -13,8 +13,8 @@ about:
   summary: SEISMIC-RNA software by the Rouskin Lab
   
 source:
-  url: https://github.com/rouskinlab/seismic-rna/archive/refs/tags/v0.21.0.tar.gz
-  sha256: f97f445ed8cee7bcdbb04476ac194ca7666efa131ab31723f1d1fe0682145e4d
+  url: https://github.com/rouskinlab/seismic-rna/archive/refs/tags/v0.21.1.tar.gz
+  sha256: 8cad84303ff0e98cbab5da6fc5e921780100cdd9ed799496cc772f85470a25e4
   
 build:
   noarch: python
diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml
index 9dfcd4bb28b7f..7fc4118201e17 100644
--- a/recipes/seqfu/meta.yaml
+++ b/recipes/seqfu/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.2" %}
-{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
+{% set version = "1.22.3" %}
+{% set sha256 = "65c1090cafe0e760e68d15d450bccfd57c0a03d553fdabca26e2191f566fef62" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml
index 04cdcf32616b4..b494ce3617d03 100644
--- a/recipes/seqwish/meta.yaml
+++ b/recipes/seqwish/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "seqwish" %}
-{% set version = "0.7.10" %}
+{% set version = "0.7.11" %}
 
 package:
   name: "{{ name }}"
@@ -7,13 +7,13 @@ package:
 
 source:
   url: https://github.com/ekg/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 133b32c9c99caf44eba955b74bae338681da78300e4b21269e07475f88c88b29
+  sha256: 9cbf51990787a93c58a1ee04239608785beb7e8a38efeb02929121b3c8c4a103
 
 build:
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x.x') }}
-  number: 1
+  number: 0
 
 requirements:
   build:
diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml
index 43ffddea1b422..6390a4c2c9a32 100644
--- a/recipes/sevenbridges-python/meta.yaml
+++ b/recipes/sevenbridges-python/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "2.11.0" %}
-{% set sha256 = "0a20b2f75cc9110adad747c0cfe7b7389b1c978008a77fae942ab66614f32534" %}
+{% set version = "2.11.1" %}
+{% set sha256 = "94f8bdd3755bbe8a461311d6281bc9cb6e5ba4861b1b99eef53b53efebe2c691" %}
 
 package:
   name: sevenbridges-python
@@ -20,6 +20,7 @@ requirements:
   host:
     - python >=3
     - pip
+    - setuptools
     - requests >=2.25.1  # needed because setup.py imports the sevenbridges module
   run:
     - python >=3
diff --git a/recipes/sfold/meta.yaml b/recipes/sfold/meta.yaml
index 6cc46554e3948..98dce74f72249 100644
--- a/recipes/sfold/meta.yaml
+++ b/recipes/sfold/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: c25e4d8cf055e13c523ef59f68c8847b66584e36359ce4fb9dc675a97f1a2939
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('sfold', max_pin='x') }}
@@ -24,6 +24,7 @@ requirements:
     - perl
     - gawk
     - grep
+    - r-cluster
 test:
   commands:
     - sfold -h  # Check if sfold command runs successfully
diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml
index b0382f7fd18a9..5357d1b2094b6 100644
--- a/recipes/smoothxg/meta.yaml
+++ b/recipes/smoothxg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "smoothxg" %}
-{% set version = "0.7.4" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 6c15c1156ac3e1a29cdb4db20f46e1b22382b22640beaa7ec8e0d76564dc53ca
+  sha256: b2b1402971c2e5cf85b318ab98583bf33f78cee33c4bcd8faa140624a76e84be
   patches:
     - CMakeLists.patch
 
diff --git a/recipes/snakedeploy/meta.yaml b/recipes/snakedeploy/meta.yaml
index 0ade185a5e11c..a65bb502853f4 100644
--- a/recipes/snakedeploy/meta.yaml
+++ b/recipes/snakedeploy/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.10.1" %}
+{% set version = "0.10.3" %}
 
 package:
   name: snakedeploy
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/snakedeploy/snakedeploy-{{ version }}.tar.gz
-  sha256: 27e14f682488d5017d52aeb6253005a51ef006b913dcb5fac217eeff70ca0c24
+  sha256: 821be1954f32d75530771f9c3fb39915068ad0987bfe3d2fc7e7f9b35b95ff78
 
 build:
   number: 0
diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml
index cd72d9426ad2d..5130d754bac38 100644
--- a/recipes/snakemake-executor-plugin-slurm/meta.yaml
+++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snakemake-executor-plugin-slurm" %}
-{% set version = "0.11.0" %}
+{% set version = "0.11.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
-  sha256: bce1df57900da71175c1c384dbc8f04d8bf8572717c0aaf95c32945a4c7a08d3
+  sha256: 293a951dcf829400bf6197705d6c602faed95aaaae9ad0d661d23b0184074134
 
 build:
   noarch: python
diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
index 56ad5ea17cf05..677f29076e7e0 100644
--- a/recipes/snakemake/meta.yaml
+++ b/recipes/snakemake/meta.yaml
@@ -1,7 +1,7 @@
 # Attention: when upgrading the version, please compare below dependencies with
 # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg
 {% set name = "snakemake" %}
-{% set version = "8.23.0" %}
+{% set version = "8.24.1" %}
 
 package:
   name: {{ name }}
@@ -9,7 +9,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz
-  sha256: 5c4348f55256eb62b2af10c64b0422ca08206193aef725b6412372a7804ef54b
+  sha256: 0559831260cdfb216d9c20f7e8465d841333935eac15f62787cec6d266efbf01
 
 build:
   number: 0
@@ -85,7 +85,7 @@ outputs:
         - setuptools
       run:
         # Keep in sync with snakemake/setup.cfg 
-        - python >=3.11,<3.13
+        - python >=3.11,<3.13 # we restrict to <3.13 because Python can have breaking changes in minor version bumps
         - appdirs
         - immutables
         - configargparse
@@ -99,18 +99,17 @@ outputs:
         - nbformat
         - packaging
         - psutil
-        - pulp >=2.3.1,<2.9
+        - pulp >=2.3.1,<2.10
         - pyyaml
-        - requests >=2.8.1
+        - requests >=2.8.1,<3.0
         - reretry
         - smart_open >=4.0,<8.0
         - snakemake-interface-executor-plugins >=9.3.2,<10.0.0
         - snakemake-interface-common >=1.17.0,<2.0
         - snakemake-interface-storage-plugins >=3.2.3,<4.0
-        - snakemake-interface-report-plugins >=1.0.0,<2.0.0
+        - snakemake-interface-report-plugins >=1.1.0,<2.0.0
         - tabulate
         - throttler
-        - toposort >=1.10,<2.0
         - wrapt
         - yte >=1.5.1,<2.0
         - dpath >=2.1.6,<3.0.0
diff --git a/recipes/snipe/meta.yaml b/recipes/snipe/meta.yaml
new file mode 100644
index 0000000000000..8bc801c964004
--- /dev/null
+++ b/recipes/snipe/meta.yaml
@@ -0,0 +1,58 @@
+{% set name = "snipe" %}
+{% set version = "0.1.4" %}
+
+package:
+  name: {{ name|lower }}
+  version: "{{ version }}"
+
+source:
+  url: https://github.com/snipe-bio/snipe/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 18f49da162e426dede11a8836b77a347e94bb618a1f0ae9eb8ae967960c81b16
+
+build:
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps -vv"
+  run_exports:
+    - {{ pin_subpackage('snipe', max_pin="x") }}
+  entry_points:
+  - snipe = snipe.cli.main:cli
+
+requirements:
+  host:
+    - python <3.12
+    - pip
+    - hatchling
+  run:
+    - python >=3.7,<3.12
+    - requests >=2.25.1
+    - click >=8.0.0
+    - numpy >=1.22,<2
+    - pathos
+    - pandas
+    - tqdm
+    - lzstring
+    - rapidfuzz
+    - zlib
+    - pyfastx >=2.1.0,<3.0a0
+    - sourmash >=4.8.11
+
+test:
+  requires:
+    - pytest
+  imports:
+    - snipe
+
+about:
+  home: "https://github.com/snipe-bio/snipe"
+  summary: "SRA-Scale sequence QC and analysis"
+  license: "AGPL-3.0-or-later"
+  license_family: "AGPL"
+  license_file: "LICENSE.txt"
+
+extra:
+  recipe-maintainers:
+    - mr-eyes
+  authors:
+    - mr-eyes
+    - drtamermanosur
diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml
index 42b89cd854fde..e0dc1cbf8c992 100644
--- a/recipes/snippy/meta.yaml
+++ b/recipes/snippy/meta.yaml
@@ -12,7 +12,7 @@ source:
   sha256: '{{ sha256 }}'
 
 build:
-  number: 4
+  number: 5
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
@@ -22,7 +22,7 @@ requirements:
     - perl
     - perl-bioperl >=1.7.2
     - bwa >=0.7.17
-    - samtools >=1.10
+    - samtools >=1.10,<=1.20
     - bcftools >=1.10
     - bedtools >=2.28.0
     - parallel >=20170422
diff --git a/recipes/splash/meta.yaml b/recipes/splash/meta.yaml
new file mode 100644
index 0000000000000..5281a849823cd
--- /dev/null
+++ b/recipes/splash/meta.yaml
@@ -0,0 +1,54 @@
+{% set name = "splash" %}
+{% set version = "2.11.0" %}
+
+{% set system = "linux" %}        # [linux]
+{% set system = "mac" %}          # [osx]
+{% set architecture = "x64" %}    # [x86_64]
+{% set architecture = "arm64" %}  # [aarch64 or arm64]
+
+{% set sha256 = "b9cfc47191ef637414b83a953ff149edde54109b31b36a7dc2d597671ebdcf3d" %} # [linux and aarch64]
+{% set sha256 = "9b2387d10ccc85aa70ed64d7d787c3d3a25add78f96be749385cccc1a01b436c" %} # [linux and x86_64]
+{% set sha256 = "59eaaf7b175e520f38f56dc6cfeaf80c894fc3b4c13ece33979f7450f3cec916" %} # [osx and arm64]
+{% set sha256 = "2eb9856a39870d02e1663daa74d7468b730ca5f2b0260e16b712c02b15dc90d4" %} # [osx and x86_64]
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/refresh-bio/SPLASH/releases/download/v{{ version }}/splash-{{ version }}.{{ system }}.{{ architecture }}.tar.gz
+  sha256:  {{ sha256 }}
+
+requirements:
+  host:
+    - python >=3.7
+  run:
+    - python >=3.7
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('splash', max_pin='x') }}
+  script: |
+    mkdir -p ${PREFIX}/bin
+    cp -r * ${PREFIX}/bin/
+
+about:
+  home: https://github.com/refresh-bio/splash
+  summary: "Unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence."
+  license: GPL-3.0-or-later
+  license_family: GPL3
+
+test:
+  commands:
+    - splash --help
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  skip-lints:
+    - should_be_noarch_generic
+    - should_not_be_noarch_source
+  identifiers:
+    - doi:10.1038/s41587-024-02381-2  
diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml
index 31fe86f18b49b..6b95c234d852a 100644
--- a/recipes/squirrel/meta.yaml
+++ b/recipes/squirrel/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.10" %}
+{% set version = "1.0.11" %}
 {% set name = "squirrel" %}
 
 package:
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz
-  sha256: f59e433906b995004f4e266235b0cfd58d80a08fd63c776d86c1846c8565254e
+  sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: python -m pip install --no-deps --ignore-installed .
   run_exports:
diff --git a/recipes/srahunter/meta.yaml b/recipes/srahunter/meta.yaml
index 2f3de29f283d5..e6e025cebedc2 100644
--- a/recipes/srahunter/meta.yaml
+++ b/recipes/srahunter/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "srahunter" %}
-{% set version = "0.0.3" %}
+{% set version = "0.0.6" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url:    https://github.com/GitEnricoNeko/srahunter/archive/refs/tags/{{version}}.tar.gz
-  sha256: f8efc31a28f84bbf62aa4b9b5b78703273ed3b6fdc29a36edc9f835838e6dd2b
+  sha256: da29cc06f8ae42506ef587a5e69ab5a4ec07fee42880f6612086fcd680531810
 build:
   entry_points:
     - srahunter=scripts.cli:main
diff --git a/recipes/steamboat/meta.yaml b/recipes/steamboat/meta.yaml
new file mode 100644
index 0000000000000..c605ef5021979
--- /dev/null
+++ b/recipes/steamboat/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "steamboat" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/steamboat-binf/steamboat_binf-{{ version }}.tar.gz
+  sha256: dfade01e251d5bbfb117378b9abeaf7231e0fc7a37fc7e37be0933ac9185981c
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv .
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - pip
+    - poetry-core
+  run:
+    - biopython
+    - executor
+    - pigz
+    - python >=3.9
+    - pyyaml
+    - rich-click >=1.6.0
+
+test:
+  imports:
+    - steamboat
+  commands:
+    - pip check
+    - gisaid-batch --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/rpetit3/steamboat-py
+  summary: A collection of tools/scripts for microbial bioinformatics
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - rpetit3
diff --git a/recipes/strainy/meta.yaml b/recipes/strainy/meta.yaml
index 756fcdc9d5669..9653b9a4f9738 100644
--- a/recipes/strainy/meta.yaml
+++ b/recipes/strainy/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.1" %}
+{% set version = "1.2" %}
 {% set name = "strainy" %}
 
 
@@ -9,11 +9,11 @@ package:
 
 source:
    url: https://github.com/katerinakazantseva/strainy/archive/refs/tags/{{ version }}.tar.gz
-   sha256: bdbac3961fa840344ac67e249de8f6d4114e0796c5b40bb5535d8e59f4dc63d1
+   sha256: 6ea476eb4a3dcbe1f1af10d2e73982b1aa57aedeedd2b688043a480052655d24
 
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: {{ PYTHON }} -m pip install -vv .
   run_exports:
@@ -51,4 +51,4 @@ about:
    license: GPL-3.0-or-later
    license_family: GPL3
    license_file: LICENSE
-   summary: assembly-based metagenomic strain phasing using long reads
+   summary: Assembly-based metagenomic strain phasing using long reads
diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml
index 82fa3b810be04..723f9b69e7bb2 100644
--- a/recipes/strangepg/meta.yaml
+++ b/recipes/strangepg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "strangepg" %}
-{% set version = "0.8.8" %}
+{% set version = "0.8.9" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 3d9accaaae14f408eb6a3f09588e79debcab122d9db9626086087fbdc9bf4b72
+  sha256: 882db3467cec22f348b8129b5730590c47fa388dbc123c972528a0a65315b5bd
 
 build:
   number: 0
diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml
index ca1e3897af0c0..599ed8367d319 100644
--- a/recipes/submission-excel2xml/meta.yaml
+++ b/recipes/submission-excel2xml/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.0" %}
+{% set version = "3.1" %}
 
 package:
   name: submission-excel2xml
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/ddbj/submission-excel2xml/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 57346c7adf11191e3163036595de96cd840978c384e851f9035cbd6f6f196f1c 
+  sha256: 30d7f49861d08c95c9a21172b881de96518447c6782b3e80d444cfda3ef81c1e 
 
 requirements:
   host:
diff --git a/recipes/svdss/build.sh b/recipes/svdss/build.sh
index 910f5cb7ec87c..cbe4e5f429877 100644
--- a/recipes/svdss/build.sh
+++ b/recipes/svdss/build.sh
@@ -1,10 +1,24 @@
-#!/usr/bin/env bash
-
-mkdir -p build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCONDAPREFIX=${PREFIX} ..
-make
-cd ..
+#!/bin/bash
 
 mkdir -p ${PREFIX}/bin
-cp SVDSS ${PREFIX}/bin
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
+	-DCMAKE_C_FLAGS="${CFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build -j "${CPU_COUNT}" -v
+
+chmod 0755 SVDSS
+mv SVDSS ${PREFIX}/bin
diff --git a/recipes/svdss/build_failure.linux-64.yaml b/recipes/svdss/build_failure.linux-64.yaml
deleted file mode 100644
index b79c12cae45be..0000000000000
--- a/recipes/svdss/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 482de6cc053f5cdae93ab4c0403880b28e0261a8aecc079bf5e3678d565bab78  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  -CONDA_BUILD_SYSROOT=
-  INFO: activate-gxx_linux-64.sh made the following environmental changes:
-  CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c
-  CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svdss-1.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c
-  DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svdss-1.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g
-  -- Using conda: -I$PREFIX/include
-  -- The C compiler identification is GNU 12.3.0
-  -- The CXX compiler identification is GNU 12.3.0
-  -- Detecting C compiler ABI info
-  -- Detecting C compiler ABI info - done
-  -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped
-  -- Detecting C compile features
-  -- Detecting C compile features - done
-  -- Detecting CXX compiler ABI info
-  -- Detecting CXX compiler ABI info - done
-  -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped
-  -- Detecting CXX compile features
-  -- Detecting CXX compile features - done
-  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-  -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-  -- Looking for pthread_create in pthreads
-  -- Looking for pthread_create in pthreads - not found
-  -- Looking for pthread_create in pthread
-  -- Looking for pthread_create in pthread - found
-  -- Found Threads: TRUE
-  -- Found OpenMP_C: -fopenmp (found version "4.5")
-  -- Found OpenMP_CXX: -fopenmp (found version "4.5")
-  -- Found OpenMP: TRUE (found version "4.5")
-  -- libdeflate from conda
-  -- htslib from conda
-  -- abpoa will be build from source (no -native)
-  -- parasail will be built from source
-  -- Configuring done (2.1s)
-  -- Generating done (0.0s)
-  -- Build files have been written to: $SRC_DIR/build
-  [  1%] Creating directories for 'ropebwt'
-  [  3%] Performing download step (git clone) for 'ropebwt'
-  Cloning into 'ropebwt'...
-  HEAD is now at bd8dbd3 Fixes compilation error (gcc 10.0.1)
-  [  5%] No update step for 'ropebwt'
-  [  7%] No patch step for 'ropebwt'
-  [  9%] No configure step for 'ropebwt'
-  [ 11%] Performing build step for 'ropebwt'
-  mrope.c: In function 'mr_restore':
-  mrope.c:149:17: warning: variable 'tot' set but not used [-Wunused-but-set-variable]
-    149 |         int64_t tot, c[6];
-        |                 ^~~
-  In file included from mrope.c:8:
-  In function 'mr_get_c',
-      inlined from 'mr_restore' at mrope.c:156:8:
-  mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds]
-     94 |                 tot = c[b];
-        |                        ~^~~
-  mrope.c: In function 'mr_restore':
-  mrope.c:149:22: note: at offset 48 into object 'c' of size 48
-    149 |         int64_t tot, c[6];
-        |                      ^
-  In file included from main.c:10:
-  In function 'mr_get_c',
-      inlined from 'main_ropebwt2' at main.c:255:3:
-  mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds]
-     94 |                 tot = c[b];
-        |                        ~^~~
-  main.c: In function 'main_ropebwt2':
-  main.c:253:25: note: at offset 48 into object 'c' of size 48
-    253 |                 int64_t c[6];
-        |                         ^
-  In function 'mr_get_c',
-      inlined from 'main_ropebwt2' at main.c:282:4:
-  mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds]
-     94 |                 tot = c[b];
-        |                        ~^~~
-  main.c: In function 'main_ropebwt2':
-  main.c:279:33: note: at offset 48 into object 'c' of size 48
-    279 |                         int64_t c[6];
-        |                                 ^
-  /opt/conda/conda-bld/svdss_1717959819873/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory
-  collect2: error: ld returned 1 exit status
-  make[3]: *** [Makefile:16: ropebwt2] Error 1
-  make[2]: *** [CMakeFiles/ropebwt.dir/build.make:86: ropebwt-prefix/src/ropebwt-stamp/ropebwt-build] Error 2
-  make[1]: *** [CMakeFiles/Makefile2:218: CMakeFiles/ropebwt.dir/all] Error 2
-  make: *** [Makefile:91: all] Error 2
-  Traceback (most recent call last):
-    File "/opt/conda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/svdss_1717959819873/work/conda_build.sh']' returned non-zero exit status 2.
-# Last 100 lines of the build log.
diff --git a/recipes/svdss/meta.yaml b/recipes/svdss/meta.yaml
index 0939c10f7364f..2fe1039f6d6bd 100644
--- a/recipes/svdss/meta.yaml
+++ b/recipes/svdss/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.5" %}
-{% set sha256 = "98345630451e98a43af9c807c9cf739cce58f6582d860ceb5daa00bdb50950df" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "825324dbdd70474b2a527925a25dea94b597ef579dee117645f285d678985652" %}
 
 package:
   name: svdss
@@ -10,8 +10,10 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 0
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('svdss', max_pin="x") }}
 
 requirements:
   build:
@@ -20,16 +22,20 @@ requirements:
     - make
     - automake
     - autoconf
-    - coreutils
-    - cmake >=3.14
+    - libtool
+    - cmake
     - git
   host:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - htslib
     - gsl
     - zlib
     - bzip2
     - xz
   run:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - samtools >=1.9
     - bcftools >=1.9
 
@@ -38,12 +44,17 @@ test:
     - SVDSS --version
 
 about:
-  home: https://github.com/Parsoa/SVDSS
+  home: "https://github.com/Parsoa/SVDSS"
   license: MIT
-  summary: Structural Variant Discovery from Sample-specific Strings
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Structural Variant Discovery from Sample-specific Strings."
+  dev_url: "https://github.com/Parsoa/SVDSS"
+  doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md"
 
 extra:
   identifiers:
     - biotools:svdss
+    - doi:10.1038/s41592-022-01674-1
   recipe-maintainers:
     - ldenti
diff --git a/recipes/tantan/meta.yaml b/recipes/tantan/meta.yaml
index 4f30f88e14745..5ddf8f7da345d 100644
--- a/recipes/tantan/meta.yaml
+++ b/recipes/tantan/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "tantan" %}
-{% set version = "50" %}
+{% set version = "51" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://gitlab.com/mcfrith/tantan/-/archive/{{ version }}/tantan-{{ version }}.tar.gz
-  sha256: a239e9fb3c059ed9eb4c25a29b3c44a2ef1c1b492a9780874f429de7ae8b5407
+  sha256: f25db9441409d526becfb10df7a610c10d0e5f163d58b21535e4f045bcfc118f
 
 build:
   number: 0
@@ -27,13 +27,13 @@ test:
     - "tantan -h"
 
 about:
-  home: https://gitlab.com/mcfrith/tantan
+  home: "https://gitlab.com/mcfrith/tantan"
   license: "GPL-3.0-or-later"
   license_family: GPL3
   license_file: "COPYING.txt"
   summary: "tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences."
-  dev_url: https://gitlab.com/mcfrith/tantan
-  doc_url: https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst
+  dev_url: "https://gitlab.com/mcfrith/tantan"
+  doc_url: "https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst"
 
 extra:
   identifiers:
diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml
index 7330003d33a96..8a164d7b20f90 100644
--- a/recipes/taxmyphage/meta.yaml
+++ b/recipes/taxmyphage/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "taxmyphage" %}
-{% set version = "0.3.2" %}
+{% set version = "0.3.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz
-  sha256: d15f63ec6a85960aeb9702dd3ad32a39808bab1c8b536a018fda1b12832ebc05
+  sha256: 89ca35ef70c214f7585960b92545c7ece75a339c252d02bec17fa28c51ccbcb8
 
 build:
   entry_points:
diff --git a/recipes/telosearchlr/build.sh b/recipes/telosearchlr/build.sh
new file mode 100644
index 0000000000000..20e19710bf486
--- /dev/null
+++ b/recipes/telosearchlr/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+for f in *.py;
+do
+  if ! grep -q "^#!/usr/bin/env python3" "$f"; then
+    sed -i "1i #!/usr/bin/env python3" "$f"
+  fi
+done
+chmod +x *.py
+mv *.py $PREFIX/bin
diff --git a/recipes/telosearchlr/meta.yaml b/recipes/telosearchlr/meta.yaml
new file mode 100644
index 0000000000000..823ff500a6125
--- /dev/null
+++ b/recipes/telosearchlr/meta.yaml
@@ -0,0 +1,36 @@
+{% set name = "TeloSearchLR" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://github.com/gchchung/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: "1f3750f062af9996aba3d0bf6ec2096e8176e9a6597fb15cb91514d5264d3225"
+
+build:
+  noarch: python
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('telosearchlr', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.9
+  run:
+    - python >=3.9
+    - Bio
+    - pillow
+    - svgutils
+    - plotly
+    - tidehunter
+
+test:
+  commands:
+    - TeloSearchLR.py -h
+about:
+  home: "https://github.com/gchchung/TeloSearchLR"
+  license: "Academic and Non-Commercial Research Use"
+  license_file: LICENSE
+  summary: "TeloSearchLR (telomere search using long sequencing reads) is a Python script for aiding the identificaiton of telomeric repeat motifs."
diff --git a/recipes/tesorter/meta.yaml b/recipes/tesorter/meta.yaml
index 5238bcacd6776..86b64e68368cd 100644
--- a/recipes/tesorter/meta.yaml
+++ b/recipes/tesorter/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "TEsorter" %}
-{% set version = "1.4.6" %}
-{% set sha256 = "c6952c98fa78d0084742fd6c7d2d1204d36db103c3cbeb19e52093cd9d311523" %}
+{% set version = "1.4.7" %}
+{% set sha256 = "f68ccedbe03fe95486d755ca1ee7d698ed3ab4779aa32ef5a2df61ca36371aae" %}
 
 package:
   name: "{{ name|lower }}"
@@ -16,7 +16,7 @@ build:
     - TEsorter = TEsorter.app:main
     - TEsorter-test = TEsorter.test.test_app:main
     - concatenate_domains.py = TEsorter.modules.concatenate_domains:main
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('tesorter', max_pin="x") }}
 
@@ -24,6 +24,7 @@ requirements:
   host:
     - python >=3
     - pip
+    - setuptools
     - hmmer
   run:
     - python >=3
@@ -44,10 +45,11 @@ about:
   license: "GPL-3.0-or-later"
   license_family: GPL3
   license_file: LICENSE
-  summary: Lineage-level classification of transposable elements using conserved protein domains.
+  summary: "Lineage-level classification of transposable elements using conserved protein domains."
   dev_url: "https://github.com/zhangrengang/TEsorter"
-  doc_url: "https://github.com/zhangrengang/TEsorter/blob/master/README.md"
+  doc_url: "https://github.com/zhangrengang/TEsorter/blob/v{{ version }}/README.md"
 
 extra:
   identifiers:
     - doi:10.1093/hr/uhac017
+    - biotools:TEsorter
diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml
index dcb55a46afbe0..fb3f66a5b43af 100644
--- a/recipes/tides-ml/meta.yaml
+++ b/recipes/tides-ml/meta.yaml
@@ -13,10 +13,10 @@ build:
   entry_points:
     - tides = tides.tides:main
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation
-  number: 0
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 1
   run_exports:
-    - {{ pin_subpackage(name, max_pin="x.x") }}
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   host:
@@ -24,16 +24,16 @@ requirements:
     - pip
   run:
     - python >=3.7,<=3.11
-    - biopython =1.79
-    - ete3 =3.1.2
-    - optuna =3.1
-    - pandas =2.0
-    - seaborn =0.12.2
-    - scikit-learn =1.5.0
-    - diamond =2.1
-    - cd-hit =4.8
-    - barrnap =0.9
-    - kraken2 =2.1
+    - biopython ==1.79
+    - ete3 >=3.1.2
+    - optuna >=3.1.1
+    - pandas ==2.1.1
+    - seaborn-base >=0.12.2
+    - scikit-learn >=1.5.0
+    - diamond >=2.1.3
+    - cd-hit >=4.8.1
+    - barrnap >=0.9
+    - kraken2 >=2.1.0
 
 test:
   imports:
@@ -47,10 +47,11 @@ test:
 
 about:
   home: https://github.com/xxmalcala/TIdeS
-  summary: Tool for ORF-calling and ORF-classification using ML approaches
+  summary: "Tool for ORF-calling and ORF-classification using ML approaches."
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/xxmalcala/TIdeS
 
 extra:
   recipe-maintainers:
diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml
index ae769341e2447..c988db6a743e4 100644
--- a/recipes/tissuumaps/meta.yaml
+++ b/recipes/tissuumaps/meta.yaml
@@ -4,7 +4,7 @@
 # - add pyqt6 (or possibly pyqt>=6) dependency
 # Until then, only the "tissuumaps_server" script is available, not "tissuumaps"
 
-{% set version = "3.2.1.10" %}
+{% set version = "3.2.1.11" %}
 
 package:
   name: tissuumaps
@@ -12,7 +12,7 @@ package:
 
 source:
   url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 126537079ea9fef743b0d2575d4e6cafac1351c465de7bbf0b0ec2b080748e34
+  sha256: 3a2e81c2e37415a6ed7e32b95b7923cef55450b5b3f2cd77fa9f2d7b12542bda
 
 build:
   number: 0
diff --git a/recipes/tower-cli/meta.yaml b/recipes/tower-cli/meta.yaml
index 4df0c97fac1f8..c20c0901b5fb6 100644
--- a/recipes/tower-cli/meta.yaml
+++ b/recipes/tower-cli/meta.yaml
@@ -1,19 +1,19 @@
 {% set name = "tw"%}
-{% set version = "0.9.2" %}
-{% set sha = "c9ebabdfe7aaeea0ce823c39819b0091503e6e8bf751281f90b620d20d365cec" %}
+{% set version = "0.10.3" %}
+{% set sha = "fe2aa1fe127196a33527f075ab23526a7fb98c00b152fa6adf32ccbc1802f2cb" %}
 
 package:
   name: tower-cli
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: generic
   run_exports:
     - {{ pin_subpackage("tower-cli", max_pin="x.x") }}
     
 source:
-  - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw.jar
+  - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw-jar.jar
     sha256: {{ sha }}
 
 requirements:
diff --git a/recipes/tower-cli/tw.sh b/recipes/tower-cli/tw.sh
index 09af6ae2257ff..c8de881445863 100644
--- a/recipes/tower-cli/tw.sh
+++ b/recipes/tower-cli/tw.sh
@@ -4,7 +4,7 @@
 set -eu -o pipefail
 
 export LC_ALL=en_US.UTF-8
-jar_file="tw.jar"
+jar_file="tw-jar.jar"
 
 # Find original directory of bash script, resolving symlinks
 # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
@@ -61,4 +61,4 @@ if [ "$jvm_mem_opts" == "" ]; then
 fi
 
 pass_arr=($pass_args)
-eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args
\ No newline at end of file
+eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args
diff --git a/recipes/trim-galore/meta.yaml b/recipes/trim-galore/meta.yaml
index dc940f7a0b079..e3194860aa232 100644
--- a/recipes/trim-galore/meta.yaml
+++ b/recipes/trim-galore/meta.yaml
@@ -10,8 +10,10 @@ source:
   sha256: '{{sha256}}'
 
 build:
-  number: 0
+  number: 1
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage("trim-galore", max_pin="x") }}
 
 requirements:
   build:
diff --git a/recipes/umicollapse/meta.yaml b/recipes/umicollapse/meta.yaml
index 3c92a82740485..ce48d66143ee4 100644
--- a/recipes/umicollapse/meta.yaml
+++ b/recipes/umicollapse/meta.yaml
@@ -1,17 +1,19 @@
-{% set name = "UMICollapse" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "40685d58f6be844ae4029eff1bf21f886f059da8293902ab390ee872e878edec"%}
+{% set name = "umicollapse" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "01b8ff5b6bcc775b277e92f5414e7e94019bfbe47fe0850810ab4e33500992b1"%}
 
 package:
-  name: umicollapse
+  name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 source:
-  url: https://github.com/CharlotteAnne/UMICollapse/archive/refs/tags/v{{ version }}.tar.gz
+  url: https://github.com/siddharthab/UMICollapse/archive/refs/tags/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
@@ -35,4 +37,4 @@ about:
     while maintaining similar functionality. This is achieved by using faster data structures with n-grams and BK-trees, 
     along other techniques that are carefully implemented to scale well to larger datasets and longer UMIs. Users of 
     UMICollapse have reported speedups from taking hours or days to run with a previous tool to taking only a few 
-    minutes with this tool with real datasets! doi 10.7717/peerj.8275.
\ No newline at end of file
+    minutes with this tool with real datasets! doi 10.7717/peerj.8275.
diff --git a/recipes/unassigner/meta.yaml b/recipes/unassigner/meta.yaml
index e3b7bce47b243..b3df994f8715f 100644
--- a/recipes/unassigner/meta.yaml
+++ b/recipes/unassigner/meta.yaml
@@ -1,46 +1,46 @@
-{% set name = "unassigner" %}
-{% set version = "1.0.0" %}
-
-package:
-  name: "{{ name|lower }}"
-  version: "{{ version }}"
-
-source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 0a79a0fdf88318a2583e2a46deffb6f6ff4ce612c55b470c007eed7bb9aa2194
-
-build:
-  number: 0
-  noarch: python
-  entry_points:
-    - unassigner = unassigner.command:main
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
-  run_exports:
-    - {{ pin_subpackage('unassigner', max_pin="x") }}
-
-requirements:
-  host:
-    - pip
-    - python
-  run:
-    - python
-    - vsearch
-    - biopython
-    - scipy
-
-test:
-  imports:
-    - unassigner
-  commands:
-    - unassigner --help
-
-about:
-  home: https://github.com/PennChopMicrobiomeProgram/unassigner
-  license: GPL-2.0-or-later
-  license_family: GPL
-  summary: "Type strain identification for 16S reads"
-  dev_url: https://github.com/PennChopMicrobiomeProgram/unassigner
-
-extra:
-  recipe-maintainers:
-    - Ulthran
+{% set name = "unassigner" %}
+{% set version = "1.0.2" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: ccfa3b95dad3db36652d73741eb7108498ac0c9664a9aef0b52cd64fd3192816
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - unassigner = unassigner.command:main
+  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  run_exports:
+    - {{ pin_subpackage('unassigner', max_pin="x") }}
+
+requirements:
+  host:
+    - pip
+    - python
+  run:
+    - python
+    - vsearch
+    - biopython
+    - scipy
+
+test:
+  imports:
+    - unassigner
+  commands:
+    - unassigner --help
+
+about:
+  home: https://github.com/PennChopMicrobiomeProgram/unassigner
+  license: GPL-2.0-or-later
+  license_family: GPL
+  summary: "Type strain identification for 16S reads"
+  dev_url: https://github.com/PennChopMicrobiomeProgram/unassigner
+
+extra:
+  recipe-maintainers:
+    - Ulthran
diff --git a/recipes/vcf-validator/LICENSE_ODB b/recipes/vcf-validator/LICENSE_ODB
deleted file mode 100644
index 52e36215fc329..0000000000000
--- a/recipes/vcf-validator/LICENSE_ODB
+++ /dev/null
@@ -1,71 +0,0 @@
-
-ODB License Exception for vcf-validator (Validator for the Variant Call
-Format (VCF)) Software
-                            Version 1.0
-
-1. Intent
-
-The intent of this License Exception is to allow the vcf-validator software
-to use ODB without the "copyleft" restrictions that would normally be
-imposed by the GPL, the license under which ODB is distributed.
-
-Specifically, the intent is to allow you to use the original vcf-validator
-software in your open source or proprietary works without imposing
-any additional restrictions to the terms and conditions of the
-Apache 2.0 license used by vcf-validator.
-
-If you wish to modify the vcf-validator software in such a way that it
-requires changes to the persistent object model handled by ODB, you can
-continue enjoying the terms of this exception provided that you are
-prepared to release your modifications under Apache 2.0 or another open
-source license and you obtain a separate license exception for your
-modifications from Code Synthesis Tools CC.
-
-While this exception is specific to vcf-validator, any open source software
-project licensed under a more liberal than the GPL license can obtain
-a similar exception free of charge by contacting Code Synthesis Tools CC.
-
-2. Definitions
-
-"Original Software" is the vcf-validator software, Copyright (c) EMBL -
-European Bioinformatics Institute, distributed under the terms of the
-Apache 2.0 license, and available to any third party from:
-
-  https://github.com/ebivariation/vcf-validator
-
-"ODB-Extended Software" are any modifications to the Original Software
-that require additions or changes to the persistent object model of
-the Original Software that is handled by ODB.
-
-"Work Based on the Original Software" is any derivative work under the
-copyright law that is either based on the Original Software or any
-modified version of the Original Software that does not constitute
-ODB-Extended Software.
-
-"Work Based on the ODB-Extended Software" is any derivative work under
-the copyright law that is based on any modified version of the Original
-Software that constitutes ODB-Extended Software.
-
-3. Legal Terms and Conditions
-
-As a special exception to the terms and conditions of version 2 of the
-GPL you may use the ODB runtime libraries in Original Software and in
-Works Based on the Original Software and distribute the resulting works
-in object code or executable form and without making source code for
-such works available to any third party, provided that all of the
-following conditions are met:
-
-  a) Original Software was licensed as a whole at no charge to all third
-     parties under the terms of the Apache 2.0 license.
-
-  b) The ODB runtime libraries in Works Based on the Original Software
-     are used solely for the purpose of supporting the functionality of
-     the Original Software.
-
-The same exception does not apply automatically to ODB-Extended Software
-or Works Based on the ODB-Extended Software. If you wish to enjoy this
-exception for such works, then you will need to license ODB-Extended
-Software at no charge to all third parties under the terms of the Apache 2.0
-license or another open source license. You will also need to obtain a
-separate License Exception for ODB-Extended Software from Code Synthesis
-Tools CC.
diff --git a/recipes/vcf-validator/build.sh b/recipes/vcf-validator/build.sh
index 7a7491a9e1988..0d0600b32e55d 100644
--- a/recipes/vcf-validator/build.sh
+++ b/recipes/vcf-validator/build.sh
@@ -1,6 +1,27 @@
-mkdir -p ${PREFIX}/bin
+#!/bin/bash
 
-mv vcf_validator* ${PREFIX}/bin/vcf_validator
-mv vcf_assembly_checker* ${PREFIX}/bin/vcf_assembly_checker
+set -x
 
-chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator
+# Set c++ to version 11
+export CXXFLAGS="-std=c++11 ${CXXFLAGS}"
+
+case $(uname -m) in 
+  aarch64 | arm64)
+    export CXXFLAGS="${CXXFLAGS} -fsigned-char" # .../vcf/compression.cpp:101:9: error: narrowing conversion of '-117' from 'int' to 'char'
+    ;;
+  *)
+    ;;
+esac
+
+mkdir build || { echo "Failed to create build directory" >&2; exit 1; }
+cd build || { echo "Failed to go into build directory" >&2; exit 1; }
+cmake -G "Unix Makefiles" -DCMAKE_CXX_FLAGS="${CXXFLAGS}" ..
+make -j"${CPU_COUNT}" || { echo "Build failed" >&2; exit 1; }
+cd .. || { echo "Failed to return to parent directory" >&2; exit 1; }
+if ! ./build/bin/test_validation_suite; then
+  echo "Validation suite failed" >&2
+  exit 1
+fi
+cp build/bin/vcf_validator ${PREFIX}/bin
+cp build/bin/vcf_assembly_checker ${PREFIX}/bin
+echo "Done with vcf-validator"
diff --git a/recipes/vcf-validator/meta.yaml b/recipes/vcf-validator/meta.yaml
index 03877f075b8f4..66ac7e00d8d62 100644
--- a/recipes/vcf-validator/meta.yaml
+++ b/recipes/vcf-validator/meta.yaml
@@ -1,25 +1,37 @@
 {% set name = "vcf-validator" %}
-{% set version = "0.9.7" %}
+{% set version = "0.10.0" %}
 
 package:
-  name: {{ name }}
+  name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_linux               # [linux]
-    sha256: 49aef4841cd7d0913ba12020465830b834ccfe20f2094222c8c41511f6c801ac                                              # [linux]
-  - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_linux        # [linux]
-    sha256: a9a00303c05c1fb5a33a5bd1f5c74fb5d8097f92a1f3ee815e19c137c0e26f13                                              # [linux]
-  - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_macos_x64           # [osx and x86]
-    sha256: 0b97a34fac6cf23951ffc33cdfb7b0602a89b4d5390564c8d816cb83019a3ffc                                              # [osx and x86]
-  - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_macos_x64    # [osx and x86]
-    sha256: 1b5404a4239da9f5e5e39bece975e4eea55d87c486121a076226829b79477bc3                                              # [osx and x86]
+  url: https://github.com/EBIvariation/vcf-validator/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: b46117700445644e6fc5a6d2655b477902c67aba0e7abe8a62df6cb49f923fff
 
 build:
-  script:
-  number: 0
+  number: 1
   run_exports:
-    - {{ pin_subpackage(name, max_pin="x.x") }}
+    - {{ pin_subpackage("vcf-validator", max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - make
+    - cmake >=2.8
+  host:
+    - libboost-devel
+    - libcurl
+    - libtool
+    - zstd
+    - c-ares
+    - openssl
+    - bzip2
+    - libzlib
+  run:
+    - zstd
+    - libcurl
 
 test:
   commands:
@@ -28,17 +40,15 @@ test:
 
 about:
   home: https://github.com/EBIVariation/vcf-validator
-  summary: EBI EVA - Validation tool to ensure VCF specification compliance
+  summary: EBI EVA - Validation tool for VCF file format compliance
   license: Apache-2.0
-  license_file:
-   - LICENSE
-   - LICENSE_ODB
+  license_file: LICENSE
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   recipe-maintainers:
     - apriltuesday
     - tcezard
-    - ebi-variation
-  skip-lints:
-    - should_be_noarch_generic
-    - should_not_be_noarch_source
+    - ebi-variation
\ No newline at end of file
diff --git a/recipes/vclust/meta.yaml b/recipes/vclust/meta.yaml
new file mode 100644
index 0000000000000..71cf91dc7c40d
--- /dev/null
+++ b/recipes/vclust/meta.yaml
@@ -0,0 +1,54 @@
+{% set version = "1.2.7" %}
+
+{% set system = "x64_linux" %}       # [linux and x86_64]
+{% set system = "x64_mac" %}         # [osx and x86_64]
+{% set system = "arm64_linux" %}     # [linux and aarch64]
+{% set system = "arm64_mac" %}       # [osx and arm64]
+
+{% set sha256 = "5f750bd1bfc8448d127ea8a566860bc10c58c768a79d3d9a814243d64c1f16cf" %}  # [linux and x86_64]
+{% set sha256 = "077a44e14e429a526868ca16364c62b800eeade9aa7df184fdda8f93e053c356" %}  # [osx and x86_64]
+{% set sha256 = "9b2b410607d26ec05b1bdc42329b73285e4a862c93f67aff6c157b10b02e3383" %}  # [linux and aarch64]
+{% set sha256 = "b917c5af92e806b4244a62a32063c81bc9de3eae3760498444398fe7c5a7f623" %}  # [osx and arm64]
+
+
+package:
+  name: vclust
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('vclust', max_pin='x') }}
+  script: |
+    mkdir -p ${PREFIX}/bin
+    cp -r vclust.py bin ${PREFIX}/bin/
+    chmod +x ${PREFIX}/bin/vclust.py
+
+source:
+  url: https://github.com/refresh-bio/vclust/releases/download/v{{ version }}/vclust-v{{ version }}-{{ system }}.tar.gz
+  sha256: {{ sha256 }}
+
+requirements:
+  host:
+    - python >=3.7
+  run:
+    - python >=3.7
+
+about:
+  home: https://github.com/refresh-bio/vclust
+  summary: "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes."
+  license: GPL-3.0-or-later
+  license_family: GPL3
+
+test:
+  commands:
+    - vclust.py --help
+    - vclust.py info
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  skip-lints:
+    - should_be_noarch_generic
+    - should_not_be_noarch_source
diff --git a/recipes/viennarna/build.sh b/recipes/viennarna/build.sh
index 7771cf62db901..2228a7c540c17 100644
--- a/recipes/viennarna/build.sh
+++ b/recipes/viennarna/build.sh
@@ -13,12 +13,10 @@ fi
             --with-cluster \
             --disable-lto \
             --without-doc \
-            --without-tutorial \
-            --without-tutorial-pdf \
             --without-cla \
             --without-rnaxplorer \
-            ${extra_config_options} \
-            && \
+            --disable-silent-rules \
+            ${extra_config_options} && \
 make -j${CPU_COUNT}
 
 ## Install
diff --git a/recipes/viennarna/fix_python_module_copy.patch b/recipes/viennarna/fix_python_module_copy.patch
new file mode 100644
index 0000000000000..bc2770d8b4818
--- /dev/null
+++ b/recipes/viennarna/fix_python_module_copy.patch
@@ -0,0 +1,28 @@
+diff -ru ViennaRNA-2.7.0/interfaces/Python/Makefile.am ViennaRNA-2.7.0/interfaces/Python/Makefile.am
+--- ViennaRNA-2.7.0/interfaces/Python/Makefile.am	2024-10-19 22:19:42.000000000 +0200
++++ ViennaRNA-2.7.0/interfaces/Python/Makefile.am	2024-10-21 22:32:45.262117727 +0200
+@@ -160,9 +160,7 @@
+   PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -O -c "from RNA import RNA" )
+ 
+ RNA/_RNA$(PYTHON3_SO): _RNA.la
+-	$(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
+-  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) RNA ) && \
+-  rm -f libtoolconfig.tmp
++	$(AM_V_GEN)( ditto `$(LIBTOOL) --config | $(SED) -n -e 's/^objdir=\(.*\)$$/\1/p'`/_RNA$(PYTHON3_SO) RNA/_RNA$(PYTHON3_SO) || cp `$(LIBTOOL) --config | $(SED) -n -e 's/^objdir=\(.*\)$$/\1/p'`/_RNA$(PYTHON3_SO) RNA/_RNA$(PYTHON3_SO) )
+ 
+ 
+ CLEANFILES = \
+diff -ru ViennaRNA-2.7.0_orig/interfaces/Python/Makefile.in ViennaRNA-2.7.0/interfaces/Python/Makefile.in
+--- ViennaRNA-2.7.0/interfaces/Python/Makefile.in	2024-10-20 12:27:41.000000000 +0200
++++ ViennaRNA-2.7.0/interfaces/Python/Makefile.in	2024-10-21 22:31:59.809208993 +0200
+@@ -1224,9 +1224,7 @@
+   PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -O -c "from RNA import RNA" )
+ 
+ RNA/_RNA$(PYTHON3_SO): _RNA.la
+-	$(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
+-  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) RNA ) && \
+-  rm -f libtoolconfig.tmp
++	$(AM_V_GEN)( ditto `$(LIBTOOL) --config | $(SED) -n -e 's/^objdir=\(.*\)$$/\1/p'`/_RNA$(PYTHON3_SO) RNA/_RNA$(PYTHON3_SO) || cp `$(LIBTOOL) --config | $(SED) -n -e 's/^objdir=\(.*\)$$/\1/p'`/_RNA$(PYTHON3_SO) RNA/_RNA$(PYTHON3_SO) )
+ 
+ all-local:  RNA/_RNA$(PYTHON3_SO)
+ 
diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml
index 13f38a0f0eae3..feb2a8c2bf757 100644
--- a/recipes/viennarna/meta.yaml
+++ b/recipes/viennarna/meta.yaml
@@ -1,30 +1,27 @@
-{% set version = "2.6.4" %}
-{% set sha256 = "d1259ce5809601a12b0dc9b724ea2c55806fece80d8d83ad417ea8a2dd574982" %}
+{% set version = "2.7.0" %}
+{% set sha256 = "9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473" %}
 
 package:
   name: viennarna
   version: {{ version }}
 
 build:
-  number: 3
+  number: 0
   run_exports:
     # Ronny said VRNA is stable in x.x releases
     - {{ pin_subpackage('viennarna', max_pin='x.x') }}
 
 source:
-  url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-{{ version }}.tar.gz
+  url: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/ViennaRNA-{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
-    - remove-register.patch
+    - fix_python_module_copy.patch
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    # pin and install swig on osx due to some incompatibility with
-    # automatically installed swig
-    - swig ==4.1.1 # [osx]
   host:
     - pkgconfig ## needed for viennarna version checks in dependent packages
     - perl
diff --git a/recipes/viennarna/remove-register.patch b/recipes/viennarna/remove-register.patch
deleted file mode 100644
index 669f253301753..0000000000000
--- a/recipes/viennarna/remove-register.patch
+++ /dev/null
@@ -1,64 +0,0 @@
-diff --git a/src/RNAlocmin/hash_util.h b/src/RNAlocmin/hash_util.h
-index e5dcfd3..50a0138 100644
---- a/src/RNAlocmin/hash_util.h
-+++ b/src/RNAlocmin/hash_util.h
-@@ -79,10 +79,10 @@ struct hash_eq {
- struct hash_fncts{
-   size_t operator()(const Structure &x) const {
- 
--  register short *k;        /* the key */
--  register unsigned  length;   /* the length of the key */
--  register unsigned  initval=0;  /* the previous hash, or an arbitrary value */
--  register unsigned a,b,c,len;
-+  short *k;        /* the key */
-+  unsigned  length;   /* the length of the key */
-+  unsigned  initval=0;  /* the previous hash, or an arbitrary value */
-+  unsigned a,b,c,len;
- 
-   /* Set up the internal state */
-   k = x.str;
-@@ -123,10 +123,10 @@ struct hash_fncts{
- 
-   size_t operator()(const struct_en &x) const {
- 
--  register short *k;        /* the key */
--  register unsigned  length;   /* the length of the key */
--  register unsigned  initval=0;  /* the previous hash, or an arbitrary value */
--  register unsigned a,b,c,len;
-+  short *k;        /* the key */
-+  unsigned  length;   /* the length of the key */
-+  unsigned  initval=0;  /* the previous hash, or an arbitrary value */
-+  unsigned a,b,c,len;
- 
-   /* Set up the internal state */
-   k = x.structure;
-@@ -165,10 +165,10 @@ struct hash_fncts{
-   return (c & HASHSIZE);
-   }
-   size_t operator()(const Structure *x) const {
--  register short *k;        /* the key */
--  register unsigned  length;   /* the length of the key */
--  register unsigned  initval=0;  /* the previous hash, or an arbitrary value */
--  register unsigned a,b,c,len;
-+  short *k;        /* the key */
-+  unsigned  length;   /* the length of the key */
-+  unsigned  initval=0;  /* the previous hash, or an arbitrary value */
-+  unsigned a,b,c,len;
- 
-   /* Set up the internal state */
-   k = x->str;
-@@ -209,10 +209,10 @@ struct hash_fncts{
- 
-   size_t operator()(const struct_en *x) const {
- 
--  register short *k;        /* the key */
--  register unsigned  length;   /* the length of the key */
--  register unsigned  initval=0;  /* the previous hash, or an arbitrary value */
--  register unsigned a,b,c,len;
-+  short *k;        /* the key */
-+  unsigned  length;   /* the length of the key */
-+  unsigned  initval=0;  /* the previous hash, or an arbitrary value */
-+  unsigned a,b,c,len;
- 
-   /* Set up the internal state */
-   k = x->structure;
diff --git a/recipes/voyager/meta.yaml b/recipes/voyager/meta.yaml
index 9fc6c50e7f52c..4a703c130333c 100755
--- a/recipes/voyager/meta.yaml
+++ b/recipes/voyager/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 {% set base = "https://bitbucket.org/sverre-phd-work/voyager/downloads" %}
-{% set sha256 = "912bf5998095095faa291d504946763e8b31da3bf3bff3a250ac51f5f214948e" %}
+{% set sha256 = "66bbfd1163b3aa5512748d99a767d378bdd45604f2e568e96c19c1c6328e42e6" %}
 
 package:
   name: voyager
diff --git a/recipes/zamp/meta.yaml b/recipes/zamp/meta.yaml
new file mode 100644
index 0000000000000..15dc951847f5f
--- /dev/null
+++ b/recipes/zamp/meta.yaml
@@ -0,0 +1,54 @@
+{% set name = "zamp" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 366d1a1bdff60e1a8100298608f20ab2294ef476a1da1bee9c1975641c495f6e
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - zamp=zamp.__main__:main
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage('zamp', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.11
+    - pip
+    - setuptools
+  run:
+    - python >=3.11
+    - snakemake-minimal >=8.0.0
+    - Click >=8.1.3
+    - attrmap >=0.0.7
+    - snaketool-utils >=0.0.5
+    - metasnek >=0.0.8
+    - biopython >=1.83
+    - pandas >=2.2.1
+    - apptainer >=1.3.2
+
+test:
+  commands:
+    - zamp -h
+    - zamp -v
+
+about:
+  home: https://github.com/metagenlab/zAMP/
+  license: MIT
+  summary: 'zAMP: bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics'
+  license_family: MIT
+  license_file: LICENSE
+
+extra:
+  container:
+    extended-base: true
+  recipe-maintainers:
+    - farchaab
+    - vicasze