diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index da43ce2168312..e5264766ba3a0 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -1,4 +1,12 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . +python_scripts=$PREFIX/lib/R/library/DEXSeq/python_scripts +sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_count.py +sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_prepare_annotation.py +chmod +x $python_scripts/dexseq_count.py +chmod +x $python_scripts/dexseq_prepare_annotation.py +mkdir -p $PREFIX/bin +ln -s $python_scripts/dexseq_count.py $PREFIX/bin/dexseq_count.py +ln -s $python_scripts/dexseq_prepare_annotation.py $PREFIX/bin/dexseq_prepare_annotation.py diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 110aae2fd7724..ce5855cbc77ba 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -5,17 +5,21 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' + source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 + build: - number: 0 + noarch: python + number: 1 rpaths: - lib/R/lib/ - lib/ + requirements: host: - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' @@ -55,13 +59,20 @@ requirements: - r-rcolorbrewer - r-statmod - r-stringr + - python <3 + - 'htseq >=0.9.1' + test: commands: - '$R -e "library(''{{ name }}'')"' + - dexseq_count.py --help + - dexseq_prepare_annotation.py --help + about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' + extra: identifiers: - biotools:dexseq