Vmatch build2 (#17262)

* Update sourmash to 2.1.0 (#17113) * Update aquila_stlfr to 1.2.9 (#17111) * Update pynnotator to add support for Python2 (#17114) * Update pynnotator to add support for Python2 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update sevenbridges-python to 0.23.1 (#17117) * Update pbmm2 to 1.1.0 (#17072) * Update pbmm2 to 1.1.0 * PacBio: Update `pbmm2` dependencies * Update nanoplot to 1.27.0 (#17118) * Update nanoget to 1.9.0 (#17116) * Update cgpbigwig to 1.0.4 (#16970) * Update cgpbigwig to 1.0.4 * Update cgpbigwig to 1.0.4 * Works on linux * just wondering... * p11-kit is linux only * Update varfish-annotator-cli to 0.10 (#17121) * Update flashlfq to 1.0.0 (#17123) * pb-falconc-0.0.1 (#17077) * pb-falconc-0.0.1 * Try to find missing gcc * Try another way CircleCI does not find "gcc", so I will try a newer way. * We are looking for gcc. Maybe this will help us find it. * Closer ``` 01:16:51 BIOCONDA INFO (OUT) echo "CC=$CC" CC=/opt/conda/conda-bld/pb-falconc_1566695732043/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc CC=$BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc ``` * alias gcc maybe? * Try symlinking gcc * further nim compilation * get nim to build * apparently this needs rsync to copy some directories. * try injecting compilers * should compile on Linux at least * better compiler injection * Update clonalframeml to 1.12 (#17120) * Update clonalframeml to 1.12 * C++, inject compilers * Adding jupyterpngsplugin python package to Bioconda (#17124) * SEPP: Update to version 4.3.10 (#16958) * Update to version 4.3.10 fix issue #70 a bug when hmmsearch fake jobs where not piped * search binaries in $PREFIX instead of relying on conda's preprocessing and replacing of /opt/anaconda1anaconda2anaconda3/ * debugging * debug a bit, this actually passes locally, possibly due to a different conda-build version * Update meta.yaml * more debugging * maybe * no slash? * not in . directories * remove debug test * Update aquila_stlfr to 1.2.10 (#17125) * Update r-bioverbs to 0.2.7 (#17127) * Update r-goalie to 0.3.6 (#17130) * Update r-syntactic to 0.2.4 (#17132) * Update angsd to 0.931 (#14862) * Update angsd to 0.929 * Update angsd to 0.931 * start simplifying * foo * tidy up * Update womtool to 45.1 (#17126) * bump platon mummer dependency version (3->4) (#17119) * Update r-transformer to 0.2.5 (#17135) * Update neurodocker to 0.5.0. (#17137) * clean and build, fail on errors, issue #11509 (#17085) * clean and build, fail on errors, issue #11509 * fix linting * This builds on linux * Update meta.yaml * Adding goenrichment python package (#17131) * Adding goenrichment python package * Update meta.yaml * bump iranges to 2.18.2 (#17138) * bump iranges to 2.18.2 * Update r-transformer * Update r-brio to 0.3.6 (#17134) * Update r-freerange to 0.2.4 (#17133) * Update r-freerange to 0.2.4 * Update meta.yaml * typo * Update r-basejump to 0.11.11 (#17136) * Update r-basejump to 0.11.11 * update dependencies * snakemake: require imagemagick >= 7.0 to avoid PDF -> PNG convert bug (#17062) * Update sevenbridges-python to 0.23.2 (#17139) Package uploads complete: [ci skip] - biocontainers/sevenbridges-python:0.23.2--py_0 - noarch/sevenbridges-python-0.23.2-py_0.tar.bz2 * Smudgeplot (#17140) * First attempt at recipe * Added R package dependencies * Added numpy dependency * Added scipy * Fixed test * Testing suggestions from PR * Final polishing after PR comments - passed local tests * Get the R stuff in the right place to ensure the pinning works * Update gridss to 2.5.2 (#17143) * Remove minepy for conda-forge/staged-recipes#9292 (#17146) * aquila first version (#17129) * first version * modify meta for bioconda install * Update meta.yaml * Update pynnotator to 1.9 (#17145) * Update pynnotator to 1.9 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update plasmidfinder to 2.1 (#17147) Package uploads complete: [ci skip] - biocontainers/plasmidfinder:2.1--0 - noarch/plasmidfinder-2.1-0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Include target dir for clean as well to ensure right location is cleane * Include target dir for clean as well to ensure right location is cleaned * bump build number * Update downpore to 0.3.3 (#12573) Package uploads complete: [ci skip] - biocontainers/downpore:0.3.3--h375a9b1_0 - linux-64/downpore-0.3.3-h375a9b1_0.tar.bz2 - osx-64/downpore-0.3.3-h375a9b1_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update gprofiler-official to 1.0.0 (#12213) Package uploads complete: [ci skip] - biocontainers/gprofiler-official:1.0.0--py_0 - noarch/gprofiler-official-1.0.0-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update rust-bio-tools to 0.6.0 (#17149) Package uploads complete: [ci skip] - biocontainers/rust-bio-tools:0.6.0--hf53bd2b_0 - linux-64/rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2 - osx-64/rust-bio-tools-0.6.0-h9904429_0.tar.bz2 * fix and update r-spieceasi (#17148) Package uploads complete: [ci skip] - biocontainers/r-spieceasi:1.0.7--r36_0 - noarch/r-spieceasi-1.0.7-r36_0.tar.bz2 Co-authored-by: Zachary Kurtz <zkurtz@lodotherapeutics.com> * Update control-freec to 11.5 (#12199) Package uploads complete: [ci skip] - biocontainers/control-freec:11.5--he1b5a44_0 - linux-64/control-freec-11.5-he1b5a44_0.tar.bz2 - osx-64/control-freec-11.5-h6de7cb9_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * minced 0.4.0 - build with older java (#17150) * Update epic2 to 0.0.40 (#17152) Package uploads complete: [ci skip] - biocontainers/epic2:0.0.40--py27h9276139_0 - biocontainers/epic2:0.0.40--py36h9276139_0 - biocontainers/epic2:0.0.40--py37h9276139_0 - linux-64/epic2-0.0.40-py27h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py36h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py37h9276139_0.tar.bz2 * Update scanpy-scripts to 0.2.4.post1 (#17151) Package uploads complete: [ci skip] - biocontainers/scanpy-scripts:0.2.4.post1--py_0 - noarch/scanpy-scripts-0.2.4.post1-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> * Update howdesbt to 1.00.03 (#16920) Package uploads complete: [ci skip] - biocontainers/howdesbt:1.00.03--hc9558a2_0 - linux-64/howdesbt-1.00.03-hc9558a2_0.tar.bz2 - osx-64/howdesbt-1.00.03-h770b8ee_0.tar.bz2 Co-authored-by: dpryan79 <dpryan79@gmail.com> Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> * Update pynnotator to 1.9.1 (#17154) Package uploads complete: [ci skip] - biocontainers/pynnotator:1.9.1--py_0 - noarch/pynnotator-1.9.1-py_0.tar.bz2 * Update paragraph to 2.3 (#16539) Package uploads complete: [ci skip] - biocontainers/paragraph:2.3--h8908b6f_0 - linux-64/paragraph-2.3-h8908b6f_0.tar.bz2 Co-authored-by: dpryan79 <dpryan79@gmail.com> Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> * Update hmmratac to 1.2.7 (#17158) Package uploads complete: [ci skip] - biocontainers/hmmratac:1.2.7--0 - noarch/hmmratac-1.2.7-0.tar.bz2 * Update libdeflate to 1.3 (#16839) * Update libdeflate to 1.3 * libdeflate has been migrated to conda-forge * Updated RNAlien to version 1.7.0 (#17153) * Updated RNAlien to version 1.7.0 * Removed echo and merged mv to one line guess the echo is for debugging and moving directly to ${t}-bin gets rid of a mv operation * Updated checksum * Fixed path * Added debug output * Fix for path * creating bin dir * creating bin dir in prefix * Minor Remove ls commands as they are debug only, added -p option to mkdir to prevent fail and only create dir if not existing * Update rnasamba to 0.1.4 (#17164) * Fix cromshell dependency (#17160) Package uploads complete: [ci skip] - biocontainers/cromshell:0.3.10--1 - noarch/cromshell-0.3.10-1.tar.bz2 * Update rnasamba to 0.1.4 (#17168) Package uploads complete: [ci skip] - biocontainers/rnasamba:0.1.4--py_0 - noarch/rnasamba-0.1.4-py_0.tar.bz2 * Update dca to 0.2.3 (#17165) Package uploads complete: [ci skip] - biocontainers/dca:0.2.3--py_0 - noarch/dca-0.2.3-py_0.tar.bz2 * Bump build number. (#17159) Package uploads complete: [ci skip] - biocontainers/pysamstats:1.1.2--py27hed695b0_5 - biocontainers/pysamstats:1.1.2--py36hed695b0_5 - biocontainers/pysamstats:1.1.2--py37hed695b0_5 - linux-64/pysamstats-1.1.2-py27hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py36hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py37hed695b0_5.tar.bz2 - osx-64/pysamstats-1.1.2-py27h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py36h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py37h2573ce8_5.tar.bz2 * Updating homer to version 4.10 and removing it from the blacklist (#17162) Package uploads complete: [ci skip] - biocontainers/homer:4.10--pl526hc9558a2_0 - linux-64/homer-4.10-pl526hc9558a2_0.tar.bz2 - osx-64/homer-4.10-pl526h770b8ee_0.tar.bz2 * Update masurca to 3.3.3 (#15706) Package uploads complete: [ci skip] - biocontainers/masurca:3.3.3--pl526haae6466_0 - linux-64/masurca-3.3.3-pl526haae6466_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update presto to 0.5.13 (#17167) Package uploads complete: [ci skip] - biocontainers/presto:0.5.13--py_0 - noarch/presto-0.5.13-py_0.tar.bz2 * Update cat to 5.0 (#17163) Package uploads complete: [ci skip] - biocontainers/cat:5.0--0 - noarch/cat-5.0-0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> * Update askocli to 0.5 (#15847) Package uploads complete: [ci skip] - biocontainers/askocli:0.5--py_0 - noarch/askocli-0.5-py_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> * Recipe for MotifBinner2 version 2.0.0 (#17141) Package uploads complete: [ci skip] - biocontainers/r-motifbinner:2.0.0--r36he1b5a44_0 - linux-64/r-motifbinner-2.0.0-r36he1b5a44_0.tar.bz2 - osx-64/r-motifbinner-2.0.0-r36h6de7cb9_0.tar.bz2 * Update breseq to 0.33.2 (#12188) Package uploads complete: [ci skip] - biocontainers/breseq:0.33.2--h8b12597_0 - linux-64/breseq-0.33.2-h8b12597_0.tar.bz2 - osx-64/breseq-0.33.2-hfbae3c0_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update spine to 0.3.2 (#12175) Package uploads complete: [ci skip] - biocontainers/spine:0.3.2--pl526_0 - noarch/spine-0.3.2-pl526_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update cwltest to 1.0.20190228134645 (#15889) Package uploads complete: [ci skip] - biocontainers/cwltest:1.0.20190228134645--py_0 - noarch/cwltest-1.0.20190228134645-py_0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@gmail.com> * Update star to 2.7.2b (#17169) * pbbam: revdep rebuilds (#17161) * Update rename to 1.601 (#17170) Package uploads complete: [ci skip] - biocontainers/rename:1.601--0 - noarch/rename-1.601-0.tar.bz2 Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com> * Update minced to 0.4.1 (#17171) Package uploads complete: [ci skip] - biocontainers/minced:0.4.1--0 - noarch/minced-0.4.1-0.tar.bz2 Co-authored-by: dpryan79 <dpryan79@gmail.com> * Update netreg to 1.8.0 (#16936) Package uploads complete: [ci skip] - biocontainers/netreg:1.8.0--h9fd3d4c_0 - linux-64/netreg-1.8.0-h9fd3d4c_0.tar.bz2 - osx-64/netreg-1.8.0-hf0ff744_0.tar.bz2 Co-authored-by: dpryan79 <dpryan79@gmail.com> * Update tadtool to 0.79 (#17173) Package uploads complete: [ci skip] - biocontainers/tadtool:0.79--py_0 - noarch/tadtool-0.79-py_0.tar.bz2 * pbbam: revdep rebuilds #2 (#17174) Package uploads complete: [ci skip] - biocontainers/bax2bam:0.0.9--h018d624_7 - biocontainers/blasr:5.3.3--h018d624_1 - linux-64/bax2bam-0.0.9-h018d624_7.tar.bz2 - linux-64/blasr-5.3.3-h018d624_1.tar.bz2 - osx-64/bax2bam-0.0.9-h13b73d5_7.tar.bz2 - osx-64/blasr-5.3.3-h13b73d5_1.tar.bz2 * Update r-exomedepth to 1.1.12 (#17175) * Update r-exomedepth to 1.1.12 * Update meta.yaml * Update mutmap to 2.1.0 (#17176) Package uploads complete: [ci skip] - biocontainers/mutmap:2.1.0--py_0 - noarch/mutmap-2.1.0-py_0.tar.bz2 * Update qtlseq to 2.0.3 (#17177) Package uploads complete: [ci skip] - biocontainers/qtlseq:2.0.3--py_0 - noarch/qtlseq-2.0.3-py_0.tar.bz2 * Update pyranges to 0.0.52 (#17178) Package uploads complete: [ci skip] - biocontainers/pyranges:0.0.52--py36h516909a_0 - biocontainers/pyranges:0.0.52--py37h516909a_0 - linux-64/pyranges-0.0.52-py36h516909a_0.tar.bz2 - linux-64/pyranges-0.0.52-py37h516909a_0.tar.bz2 - osx-64/pyranges-0.0.52-py36h01d97ff_0.tar.bz2 - osx-64/pyranges-0.0.52-py37h01d97ff_0.tar.bz2 * simka-1.5.0 (#16670) * simka-1.5.0 * Update mobidic-mpa to 1.1.2 (#17181) Package uploads complete: [ci skip] - biocontainers/mobidic-mpa:1.1.2--py_0 - noarch/mobidic-mpa-1.1.2-py_0.tar.bz2 * Update popdel to 1.1.2 (#17182) Package uploads complete: [ci skip] - biocontainers/popdel:1.1.2--he513fc3_0 - linux-64/popdel-1.1.2-he513fc3_0.tar.bz2 - osx-64/popdel-1.1.2-h2dec4b4_0.tar.bz2 * Create variable (this has been removed in 7624ae9 by mistake). * Set shell options. * Set shebang and shell options. * Use a HEREDOC for ${PREFIX}/.message.txt. * Bump build number. * Remove blank line. * I wonder * guess that didn't work
bioconda · Sep 7, 2019 · 64b68de · 64b68de
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -23,7 +23,6 @@ recipes/circulator
 recipes/igdiscover
 recipes/rnftools
 recipes/tiptoft
-recipes/homer
 recipes/emboss
 recipes/embassy-phylip
 recipes/triform2
@@ -629,7 +628,6 @@ recipes/r-rBLAST
 recipes/r-rubic
 recipes/r-scimpute
 recipes/r-soap-nmr
-recipes/r-spieceasi
 recipes/r-xmlrpc
 recipes/r-zerone
 

diff --git a/recipes/angsd/build.sh b/recipes/angsd/build.sh
@@ -1,26 +1,3 @@
 #! /bin/bash
-binaries="\
-misc/msToGlf \
-misc/contamination \
-misc/contamination2 \
-misc/splitgl \
-misc/thetaStat \
-misc/printIcounts \
-misc/NGSadmix \
-misc/realSFS \
-misc/smartCount \
-misc/supersim \
-angsd \
-"
-BINDIR=$PREFIX/bin
-mkdir -p $BINDIR
-
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPP_INCLUDE_PATH=${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${PREFIX}/include
-export CXX_INCLUDE_PATH=${PREFIX}/include
-export LIBRARY_PATH=${PREFIX}/lib
-# needed because it is otherwise reported that SIZE_MAX is undefined
-make FLAGS="-O3 -D__WITH_POOL__ -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS "
-
-for i in $binaries; do cp $i $BINDIR && chmod +x $BINDIR/$(basename $i); done
+mkdir -p ${PREFIX}/bin
+make CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" prefix=$PREFIX CC=$CC CXX=$CXX install
diff --git a/recipes/angsd/meta.yaml b/recipes/angsd/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.923" %}
-{% set sha256 = "5144c16c901faa9dd9310c04f391df2ef2a5f7ddfcded4d9fba609279715c9c6" %}
+{% set version = "0.931" %}
+{% set sha256 = "9f1a7e769ca2b5b3df33c0c27313cba4cb7af9b2c41213b5cc10a88d85635350" %}
 
 package:
   name: angsd

diff --git a/recipes/aquila/meta.yaml b/recipes/aquila/meta.yaml
@@ -0,0 +1,44 @@
+{% set name = "aquila" %}
+{% set version = "1.0.0" %}
+
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
+
+source:
+  url: https://github.com/xinzhoucs/Aquila/archive/v{{ version }}.tar.gz
+  sha256: 035da84ffc116ce6a9cf5bdd2d53428efa2d84fd5c9009c94cc9c700410cc542
+
+requirements:
+  host:
+    - python >=3
+    - pip
+  run:
+    - python >=3
+    - samtools
+    - pysam >=0.15.2
+    - minimap2
+    - scipy
+    - numpy
+
+test:
+  commands:
+    - Aquila_step1 --help
+    - Aquila_step2 --help
+    - Aquila_clean --help
+    - Aquila_step1_multilibs --help
+    - Aquila_assembly_based_variants_call --help
+    - Aquila_phasing_all_variants --help
+    - Aquila_step0_sortbam --help
+    - Aquila_step0_sortbam_multilibs --help
+
+about:
+  home: https://github.com/maiziex/Aquila
+  license: MIT
+  summary: Diploid personal genome assembly and comprehensive variant detection based on linked-reads
diff --git a/recipes/aquila_stlfr/meta.yaml b/recipes/aquila_stlfr/meta.yaml
@@ -1,15 +1,15 @@
 package:  
   name: aquila_stlfr
-  version: "1.2.8"
+  version: "1.2.10"
 
 build:
   noarch: python
   number: 0
   script: python setup.py install --single-version-externally-managed --record=record.txt
 
 source:
-  url: https://github.com/xinzhoucs/Aquila_stLFR/archive/v1.2.8.tar.gz
-  sha256: 403363cf1d4c2ead229480a1b619f482d6d74e4c888f29fd6e97025c9d2a265e
+  url: https://github.com/xinzhoucs/Aquila_stLFR/archive/v1.2.10.tar.gz
+  sha256: 31e0a981bf427c372f5bffe2f821e929b4c0c073b949b99cd4160114896e4b23
 
 requirements:
   host:

diff --git a/recipes/askocli/meta.yaml b/recipes/askocli/meta.yaml
@@ -1,13 +1,14 @@
 package:
   name: askocli
-  version: "0.4.3"
+  version: "0.5"
 
 build:
-  number: 1
+  number: 0
+  noarch: python
 
 source:
-  url: https://pypi.python.org/packages/e3/3a/e281d5400338292995443eb60c847d952b0605a871efb224a22ecc0aea82/askocli-0.4.3.tar.gz
-  md5: 730e1587650ba41f7d4c2b77ad96a987
+  url: https://files.pythonhosted.org/packages/e3/e2/fdbe6e74bd713aec7334d923f2e2298382fa8201798f3645917828fc4dc0/askocli-0.5.tar.gz
+  sha256: 5d4fa3d0cbb5962da766e7c0b4b5fc4cbe46f2bd8438b8e5a9a6f50f77745cad
 
 requirements:
   host:

diff --git a/recipes/bam2fastx/meta.yaml b/recipes/bam2fastx/meta.yaml
@@ -21,7 +21,7 @@ extra:
     - mhsieh
 
 build:
-  number: 7
+  number: 8
 
 requirements:
   build:
@@ -32,11 +32,11 @@ requirements:
   host:
     - boost
     - zlib
-    - pbbam 0.23.0*
-    - pbcopper 0.4.2*
+    - pbbam 1.0.6*
+    - pbcopper 1.3.0*
   run:
-    - pbbam 0.23.0*
-    - pbcopper 0.4.2*
+    - pbbam 1.0.6*
+    - pbcopper 1.3.0*
 
 test:
   commands:

diff --git a/recipes/bax2bam/build.sh b/recipes/bax2bam/build.sh
@@ -4,8 +4,12 @@ export BOOST_ROOT="${PREFIX}"
 export PKG_CONFIG_LIBDIR="${PREFIX}"/lib/pkgconfig
 
 # HDF5 doesn't have pkgconfig files yet
-export CPPFLAGS="-isystem ${PREFIX}/include"
-export LDFLAGS="-L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+export CPPFLAGS+=" -isystem ${PREFIX}/include"
+export LDFLAGS+=" -L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+
+# required for Meson's sanity check
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib"
 
 # configure
 # '--wrap-mode nofallback' prevents meson from downloading

diff --git a/recipes/bax2bam/meta.yaml b/recipes/bax2bam/meta.yaml
@@ -21,7 +21,7 @@ extra:
     - mhsieh
 
 build:
-  number: 6
+  number: 7
 
 requirements:
   build:
@@ -34,12 +34,12 @@ requirements:
     - hdf5
     - zlib
     - blasr_libcpp 5.3.3*
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
   run:
     - hdf5
     - zlib
     - blasr_libcpp 5.3.3*
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
 
 test:
   commands:

diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.18.1" %}
+{% set version = "2.18.2" %}
 {% set name = "IRanges" %}
 {% set bioc = "3.9" %}
 
@@ -10,7 +10,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: b549e2cc12cef49b47a4a8e1b71608b2
+  md5: 4d4c5bf8506ded6e85e48a09983fd4a8
 build:
   number: 0
   rpaths:

diff --git a/recipes/blasr/build.sh b/recipes/blasr/build.sh
@@ -4,8 +4,12 @@ export BOOST_ROOT="${PREFIX}"
 export PKG_CONFIG_LIBDIR="${PREFIX}"/lib/pkgconfig
 
 # HDF5 doesn't have pkgconfig files yet
-export CPPFLAGS="-isystem ${PREFIX}/include"
-export LDFLAGS="-L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+export CPPFLAGS+=" -isystem ${PREFIX}/include"
+export LDFLAGS+=" -L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+
+# required for Meson's sanity check
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib"
 
 # configure
 # '--wrap-mode nofallback' prevents meson from downloading

diff --git a/recipes/blasr/meta.yaml b/recipes/blasr/meta.yaml
@@ -21,7 +21,7 @@ extra:
     - mhsieh
 
 build:
-  number: 0
+  number: 1
 
 requirements:
   build:
@@ -34,11 +34,11 @@ requirements:
     - zlib
     - hdf5
     - blasr_libcpp 5.3.3*
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
   run:
     - hdf5
     - blasr_libcpp 5.3.3*
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
 
 test:
   commands:

diff --git a/recipes/blasr_libcpp/build.sh b/recipes/blasr_libcpp/build.sh
@@ -4,8 +4,12 @@ export BOOST_ROOT="${PREFIX}"
 export PKG_CONFIG_LIBDIR="${PREFIX}"/lib/pkgconfig
 
 # HDF5 doesn't have pkgconfig files yet
-export CPPFLAGS="-isystem ${PREFIX}/include"
-export LDFLAGS="-L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+export CPPFLAGS+=" -isystem ${PREFIX}/include"
+export LDFLAGS+=" -L${PREFIX}/lib -lhdf5_cpp -lhdf5"
+
+# required for Meson's sanity check
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib"
 
 # configure
 # '--wrap-mode nofallback' prevents meson from downloading

diff --git a/recipes/blasr_libcpp/meta.yaml b/recipes/blasr_libcpp/meta.yaml
@@ -21,7 +21,7 @@ extra:
     - mhsieh
 
 build:
-  number: 0
+  number: 1
 
 requirements:
   build:
@@ -33,10 +33,10 @@ requirements:
     - boost
     - zlib
     - hdf5
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
   run:
     - hdf5
-    - pbbam 0.23.0*
+    - pbbam 1.0.6*
 
 test:
   commands:

diff --git a/recipes/breseq/build.sh b/recipes/breseq/build.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+set -eux
+./configure --prefix=$PREFIX
+make
+make install
diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.33.0" %}
-{% set sha256 = "f553931e810a5c31434f2f90e977589c99c9dcbd258045df9fd37acc21d58574" %}
+{% set version = "0.33.2" %}
+{% set sha256 = "ce1cb0c2893bdec4736e667214be47282d14bfb7d5fcefa097c342ca22e9082e" %}
 
 package:
   name: breseq
@@ -13,11 +13,11 @@ source:
 
 build:
   number: 0
-  script: ./configure --prefix=$PREFIX && make && make install
 
 requirements:
   build:
     - '{{ compiler("c") }}'
+    - '{{ compiler("cxx") }}'
   host:
     - zlib
   run:

diff --git a/recipes/canu/build.sh b/recipes/canu/build.sh
@@ -1,10 +1,13 @@
 #!/bin/bash
 
-mkdir -p "$PREFIX/libexec" "$PREFIX/bin"
+# fail on all errors
+set -e
 
-# Build Canu into libexec dir
-( cd src; make TARGET_DIR=$PREFIX/libexec )
+mkdir -p "$PREFIX/bin"
 
-# Link all executable files to bin
-find $PREFIX/libexec -type f -perm +111 -exec ln -s {} $PREFIX/bin \;
+pushd src
+make clean TARGET_DIR=$PREFIX CC=$CC CXX=$CXX
+make TARGET_DIR=$PREFIX CC=$CC CXX=$CXX
 
+# This installs all of the object files as well, remove that
+rm -rf $PREFIX/*amd64
diff --git a/recipes/canu/meta.yaml b/recipes/canu/meta.yaml
@@ -6,20 +6,19 @@ package:
   version: '{{version}}'
 
 source:
-  # Canu currently needs to come from git to get its version string right
   url: https://github.com/marbl/canu/archive/v{{version}}.tar.gz
   sha256: '{{sha256}}'
 
 build:
-  number: 0
-  skip: true  # [osx]
-  detect_binary_files_with_prefix: true
+  number: 2
+  # This should actually work, but it explicitly checks for gcc
+  skip: True  # [osx]
 
 requirements:
   build:
     - '{{ compiler("c") }}'
+    - '{{ compiler("cxx") }}'
   host:
-    - perl
     - gnuplot >=5.0.5
   run:
     - perl
@@ -34,6 +33,7 @@ test:
 about:
   home: http://canu.readthedocs.org/
   license: GPLv2 and others
+  license_file: README.licenses
   license_family: GPL
   summary: Canu is a fork of the Celera Assembler designed for high-noise single-molecule
     sequencing.

diff --git a/recipes/cat/meta.yaml b/recipes/cat/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "4.6" %}
-{% set sha256 = "e3accfcdef261647081125e11581a7aa7d0bfb8583b341334b5bffd9c2f88db4" %}
+{% set version = "5.0" %}
+{% set sha256 = "c1ef76d4e23e48111f15627d5a388edaca8d6e814c093fd20029457cc28175ad" %}
 
 package:
   name: cat
@@ -11,10 +11,11 @@ source:
 
 build:
   number: 0
+  noarch: generic
 
 requirements:
   run:
-    - python=3
+    - python 3
     - diamond
     - prodigal