diff --git a/recipes/fastqc/0.11.7/build.sh b/recipes/fastqc/0.11.7/build.sh new file mode 100644 index 0000000000000..6e5d5beb7a3df --- /dev/null +++ b/recipes/fastqc/0.11.7/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +fastqc=$PREFIX/opt/$PKG_NAME-$PKG_VERSION +mkdir -p $fastqc +cp -r ./* $fastqc +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $fastqc/fastqc +rm -f $fastqc/fastqc.bak +chmod +x $fastqc/fastqc +mkdir -p $PREFIX/bin +ln -s $fastqc/fastqc $PREFIX/bin/fastqc + diff --git a/recipes/fastqc/0.11.7/java_xms.patch b/recipes/fastqc/0.11.7/java_xms.patch new file mode 100644 index 0000000000000..e3b72952d4bd7 --- /dev/null +++ b/recipes/fastqc/0.11.7/java_xms.patch @@ -0,0 +1,18 @@ +*** fastqc.orig 2015-10-09 11:59:24.000000000 -0400 +--- fastqc 2015-12-16 13:27:53.953520316 -0500 +*************** +*** 158,167 **** +--- 158,170 ---- + + push @java_args ,"-Dfastqc.threads=$threads"; + my $memory = 250 * $threads; ++ my $stack = 200 * $threads; + unshift @java_args,"-Xmx${memory}m"; ++ unshift @java_args,"-Xms${memory}m"; + } + else { + unshift @java_args,'-Xmx250m'; ++ unshift @java_args,'-Xms200m'; + } + + if ($kmer_size) { diff --git a/recipes/fastqc/0.11.7/meta.yaml b/recipes/fastqc/0.11.7/meta.yaml new file mode 100644 index 0000000000000..4dc5f6964a572 --- /dev/null +++ b/recipes/fastqc/0.11.7/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "fastqc" %} +{% set version = "0.11.7" %} +{% set sha256hash = "59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: http://www.bioinformatics.babraham.ac.uk/projects/{{ name }}/{{ name }}_v{{ version }}.zip + sha256: {{ sha256hash }} + patches: + - java_xms.patch + +build: + detect_binary_files_with_prefix: true + number: 5 + +requirements: + run: + # Enforce a version requirement on openjdk to ensure + # it comes from the conda-forge channel and not default. + # Many yaks were shaved to bring us this information. + # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906 + - openjdk >=8.0.144 + - perl + +test: + commands: + - fastqc -h + - fastqc --version + +about: + home: 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' + license: GPL >=3 + summary: 'A quality control tool for high throughput sequence data.' + +extra: + identifiers: + - biotools:fastqc diff --git a/recipes/fastqc/meta.yaml b/recipes/fastqc/meta.yaml index 4dc5f6964a572..e7b71e8e15372 100644 --- a/recipes/fastqc/meta.yaml +++ b/recipes/fastqc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "fastqc" %} -{% set version = "0.11.7" %} -{% set sha256hash = "59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112" %} +{% set version = "0.11.8" %} +{% set sha256hash = "ca87fe77807e4ac796b6cad949858921fd20652c4038f586f05ece94b5022129" %} package: name: {{ name|lower }} @@ -14,7 +14,7 @@ source: build: detect_binary_files_with_prefix: true - number: 5 + number: 0 requirements: run: