bioconda · dpryan79 · Oct 11, 2019 · Dec 29, 2018 · Dec 30, 2018 · Dec 30, 2018
diff --git a/build-fail-blacklist b/build-fail-blacklist
diff --git a/recipes/a5-miseq/build.sh b/recipes/a5-miseq/build.sh
@@ -6,4 +6,5 @@ mkdir -p $A5_MISEQ_HOME
 cp -R $SRC_DIR/* $A5_MISEQ_HOME/
 
 # Create symbolic links for a5_miseq's launch script
-ln -s $A5_MISEQ_HOME/bin/a5_pipeline.pl $BINARY_HOME/ 
+mkdir -p $BINARY_HOME
+ln -s $A5_MISEQ_HOME/bin/a5_pipeline.pl $BINARY_HOME/ 
diff --git a/recipes/assemblerflow/meta.yaml b/recipes/assemblerflow/meta.yaml
@@ -6,7 +6,7 @@ package:
   version: '{{ version }}'
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }}
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: b0390727602e90dad1c3afa8dd408e5c30471a0f6d35b323989e9df4e8aa70fb
 
 build:

diff --git a/recipes/bs-seeker2/meta.yaml b/recipes/bs-seeker2/meta.yaml
@@ -1,14 +1,16 @@
+{% set version = "2.1.0" %}
+
 package:
   name: bs-seeker2
-  version: "2.1.0"
+  version: {{ version }}
 
 build:
   noarch: generic
   number: 1
 
 source:
-  url: http://pellegrini.mcdb.ucla.edu/BS_Seeker2/BSseeker2_v2.1.0.tar.bz
-  md5: 2f3cb74a75453140f20e396ee68402bf
+  url: https://github.com/BSSeeker/BSseeker2/archive/v{{ version }}.tar.gz
+  sha256: 9eaeba3e15db18aa69c2466d4915dbdc8e99853b63dc17119501367f4bfd3996
 
 requirements:
   run:

diff --git a/recipes/bwise/build.sh b/recipes/bwise/build.sh
@@ -1,14 +1,13 @@
 #!/bin/bash
 
-cd src;
-make;
+cd src
+make CC=${CXX} CFLAGS="$CXXFLAGS -fopenmp -L${PREFIX}/lib -lz" LDFLAGS="-L${PREFIX}/lib -flto -fopenmp -lz"
 
-
-mkdir -p $PREFIX/bin;
-cp src/path_counter Bwise_path_counter;
-cp src/path_to_kmer Bwise_path_to_kmer;
-cp src/maximal_sr Bwise_maximal_sr;
-cp src/K2000/K2000.py Bwise_K2000.py;
-cp src/K2000/K2000_msr_to_gfa.py Bwise_K2000_msr_to_gfa.py;
-cp src/K2000/K2000_gfa_to_fasta.py Bwise_K2000_gfa_to_fasta.py;
-cp src/Bwise_conda $PREFIX/bin/bwise;
+mkdir -p $PREFIX/bin
+cp path_counter Bwise_path_counter
+cp path_to_kmer Bwise_path_to_kmer
+cp maximal_sr Bwise_maximal_sr
+cp K2000/K2000.py Bwise_K2000.py
+cp K2000/K2000_msr_to_gfa.py Bwise_K2000_msr_to_gfa.py
+cp K2000/K2000_gfa_to_fasta.py Bwise_K2000_gfa_to_fasta.py
+cp Bwise_conda $PREFIX/bin/bwise
diff --git a/recipes/bwise/meta.yaml b/recipes/bwise/meta.yaml
@@ -17,16 +17,18 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-
+  host:
+    - zlib
   run:
     - python >=3
     - bgreat
     - bcalm
     - btrim
+    - zlib
 
 test:
   commands:
-    - bwise
+    - bwise --help
 
 about:
   home: https://github.com/Malfoy/BWISE

diff --git a/recipes/clearcut/build.sh b/recipes/clearcut/build.sh
@@ -1,4 +1,4 @@
-mkdir -pv ${PREFIX}/bin
+mkdir -p ${PREFIX}/bin
 cd clearcut
 make 
 cp clearcut ${PREFIX}/bin
diff --git a/recipes/clearcut/meta.yaml b/recipes/clearcut/meta.yaml
@@ -8,6 +8,7 @@ source:
 
 build:
   number: 1
+  skip: True  # [osx]
 
 requirements:
   build:

diff --git a/recipes/commet/build.sh b/recipes/commet/build.sh
@@ -3,7 +3,7 @@
 mkdir -p ${PREFIX}/bin
 
 # installation
-make
+make CC=$CXX CFLAGS="$CXXFLAGS -Iinclude -L${PREFIX}/lib"
 
 # copy binaries and scripts
 cp Commet.py ${PREFIX}/bin

diff --git a/recipes/commet/meta.yaml b/recipes/commet/meta.yaml
@@ -17,10 +17,13 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
   host:
     - r-base
+    - zlib
   run:
+    - zlib
     - r-base
     - r-gplots
     - python

diff --git a/recipes/fusion-inspector/meta.yaml b/recipes/fusion-inspector/meta.yaml
@@ -1,5 +1,6 @@
 {% set name = "fusion-inspector" %}
 {% set version = "1.3.1" %}
+{% set build = "1" %}
 
 package:
   name: {{ name }}
@@ -11,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: {{ build }}
   # The reason for skipping osx is that trinity >=2.4 is not available in the osx channel
   # The python code in FusionInspector runs on python 2.7.
 

diff --git a/recipes/lsc/meta.yaml b/recipes/lsc/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "2.0"
 
 source:
-  url: https://www.healthcare.uiowa.edu/labs/au/LSC/files/LSC-2.0.tar.gz
+  url: http://augroup.org/LSC/files/LSC-2.0.tar.gz
   md5: 10e0e85f74a7975cd46ef4ea43ab7c5d
   patches:
     - install_paths.patch

diff --git a/recipes/mirdeep2/build.sh b/recipes/mirdeep2/build.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+mkdir -p $PREFIX/bin
 cp src/* $PREFIX/bin
 
 cp Rfam_for_miRDeep.fa $PREFIX/bin

diff --git a/recipes/mirdeep2/meta.yaml b/recipes/mirdeep2/meta.yaml
@@ -1,10 +1,11 @@
+#The actual version is x.y.z in 2.x.y.z
 package:
   name: mirdeep2
   version: '2.0.0.8'
 
 source:
-  url: https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip
-  md5: a707f7d7ad4a2975fb8b2e78c5bcf483
+  url: https://github.com/rajewsky-lab/mirdeep2/archive/v0.0.8.tar.gz
+  sha256: 62762e99d4b095a0fd822e964d213729236ffc53c425121b6835c2d76e84a072
   patches:
     - mirdeep2.patch
 

diff --git a/recipes/mqc/build.sh b/recipes/mqc/build.sh
@@ -1,8 +1,8 @@
 #! /bin/bash
 
+mkdir -p $PREFIX/bin/mqc_tools
 cp mQC.pl $PREFIX/bin
 chmod +x $PREFIX/bin/mQC.pl
-mkdir $PREFIX/bin/mqc_tools
 cp mqc_tools/*.py $PREFIX/bin/mqc_tools
 chmod +x $PREFIX/bin/mqc_tools/*.py
 cp mqc_tools/*.R $PREFIX/bin/mqc_tools

diff --git a/recipes/msms/meta.yaml b/recipes/msms/meta.yaml
@@ -8,12 +8,12 @@ package:
 source:
   - url: {{ url_base }}/REL{{ version }}/msms_i86_64Linux2_{{ version }}.tar.gz  # [linux]
     md5: 650d8c6fd49d9ce291f30ed530d5f313  # [linux]
-    patches:
+    patches:  # [linux]
       - pdb_to_xyzr.patch  # [linux]
       - pdb_to_xyzrn.patch  # [linux]
   - url: {{ url_base }}/REL{{ version }}/msms_MacOSX_{{ version }}.tar.gz      # [osx]
     md5: 36bd8447908d12a8703f458564cbe74b  # [osx]
-    patches:
+    patches:  # [osx]
       - pdb_to_xyzr.patch  # [osx]
       - pdb_to_xyzrn.patch  # [osx]
 

diff --git a/recipes/novoalign/meta.yaml b/recipes/novoalign/meta.yaml
@@ -11,11 +11,11 @@ package:
 source:
   - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.Linux2.6.32.tar.gz  # [linux]
     sha256: {{ sha256_linux }}  # [linux]
-    patches:
+    patches:  # [linux]
       - 0001-patches-for-compiling-novo2maq.patch  # [linux]
   - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.MacOSX.tar.gz  # [osx]
     sha256: {{ sha256_osx }}  # [osx]
-    patches:
+    patches: # [osx]
       - 0001-patches-for-compiling-novo2maq.patch  # [osx]
 
 build:

diff --git a/recipes/probamconvert/build.sh b/recipes/probamconvert/build.sh
@@ -1,3 +1,4 @@
 #!/bin/bash
 
+mkdir -p ${PREFIX}/bin
 cp python/*.py $PREFIX/bin/
diff --git a/recipes/r-quorts/build.sh b/recipes/r-quorts/build.sh
diff --git a/recipes/r-quorts/meta.yaml b/recipes/r-quorts/meta.yaml
diff --git a/recipes/rapid/v0.7/build.sh b/recipes/rapid/v0.7/build.sh
diff --git a/recipes/rapid/v0.7/meta.yaml b/recipes/rapid/v0.7/meta.yaml
diff --git a/recipes/s3gof3r/meta.yaml b/recipes/s3gof3r/meta.yaml
@@ -4,9 +4,9 @@ package:
 
 source:
   - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_linux_amd64.tar.gz # [linux]
-    sha256: d88f199d1580d8c8cac26ba39e15dc6e2126d20e56c3894bd37a226e8b3e665c
+    sha256: d88f199d1580d8c8cac26ba39e15dc6e2126d20e56c3894bd37a226e8b3e665c  # [linux]
   - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_darwin_amd64.zip # [osx]
-    sha256: 85ace61bd58cf57034e748af22b8a3c9ca82ed194da3a4c1c646989d78ee2947
+    sha256: 85ace61bd58cf57034e748af22b8a3c9ca82ed194da3a4c1c646989d78ee2947  # [osx]
 
 build:
   number: 1

diff --git a/recipes/seqprep/1.1/build.sh b/recipes/seqprep/1.1/build.sh
@@ -1,3 +1,3 @@
 mkdir -p ${PREFIX}/bin
-make
+make CC=$CC CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS -lz -lm"
 cp SeqPrep ${PREFIX}/bin
diff --git a/recipes/spades/3.10.1/meta.yaml b/recipes/spades/3.10.1/meta.yaml
@@ -17,7 +17,7 @@ requirements:
 
 test:
   commands:
-    - spades.py --test
+    - spades.py --test && rm -rf spades_test
 
 about:
   home: http://bioinf.spbau.ru/en/spades

diff --git a/recipes/spades/3.9.0/meta.yaml b/recipes/spades/3.9.0/meta.yaml
@@ -9,6 +9,7 @@ source:
     md5: 9e4d280fefe67589c028170fcb6749b3                                      # [osx]
 
 build:
+  skip: True  # [osx]
   number: 3
 
 requirements:

diff --git a/recipes/virema/build.sh b/recipes/virema/build.sh
@@ -1,4 +1,6 @@
 #!/bin/bash
 
+mkdir -p ${PREFIX}/bin
+head -n 2 *.py
 cp *.py $PREFIX/bin
 chmod +x $PREFIX/bin/*
diff --git a/recipes/virema/path.patch b/recipes/virema/path.patch
@@ -1,14 +1,14 @@
---- ViReMa_0.6/ViReMa.py	2014-06-25 12:43:38.000000000 +0000
-+++ ViReMa_0.6/ViReMa.py.new	2017-09-14 16:09:13.112629345 +0000
+--- ViReMa.py	2014-06-25 12:43:38.000000000 +0000
++++ ViReMa.py	2017-09-14 16:09:13.112629345 +0000
 @@ -1,3 +1,4 @@
-+#!/usr/bin/env python
++#!/usr/bin/env python
  ##      Copyright (c) 2013-2014 Andrew Laurence Routh
  ##      
  ##      Permission is hereby granted, free of charge, to any person obtaining a copy
---- ViReMa_0.6/Compiler_Module.py	2014-06-25 13:36:30.000000000 +0000
-+++ ViReMa_0.6/Compiler_Module.py.new	2017-09-14 16:09:27.678753883 +0000
+--- Compiler_Module.py	2014-06-25 13:36:30.000000000 +0000
++++ Compiler_Module.py	2017-09-14 16:09:27.678753883 +0000
 @@ -1,3 +1,4 @@
-+#!/usr/bin/env python
++#!/usr/bin/env python
  ##      Copyright (c) 2013-2014 Andrew Laurence Routh
  ##      
  ##      Permission is hereby granted, free of charge, to any person obtaining a copy
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,7 @@ source: @@
     build:
       number: 1
+      skip: True  # [osx]
     requirements:
       build:
@@ Expand Down @@