From 9d7a773ce1ec2e8f348be66f960e525cdbbde584 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 27 Nov 2018 10:31:37 -0500 Subject: [PATCH 1/5] Restore dexseq python helper scripts --- recipes/bioconductor-dexseq/build.sh | 14 +++++++++++++- recipes/bioconductor-dexseq/meta.yaml | 4 +++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index da43ce2168312..7c45ac75b66b0 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -1,4 +1,16 @@ #!/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' $python_scripts/dexseq_prepare_annotation.py +if [ "$PY3K" == 1 ]; then + 2to3 -w $python_scripts/dexseq_count.py + 2to3 -w $python_scripts/dexseq_prepare_annotation.py +fi +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 $PREFIX/bin/dexseq_prepare_annotation.py diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 110aae2fd7724..764463c772593 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -58,6 +58,8 @@ requirements: test: commands: - '$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)' From cad646d4f0907cbd4ec0508a2ffe5dd8be80a260 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 27 Nov 2018 10:57:19 -0500 Subject: [PATCH 2/5] Add python requirement for helper scripts --- recipes/bioconductor-dexseq/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 764463c772593..c339f61b4e0c3 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -55,6 +55,7 @@ requirements: - r-rcolorbrewer - r-statmod - r-stringr + - python test: commands: - '$R -e "library(''{{ name }}'')"' From 4110643e2ac68a6b0b36eec68d61bdec3dea99ab Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 27 Nov 2018 10:59:41 -0500 Subject: [PATCH 3/5] Add python noarch to build section --- recipes/bioconductor-dexseq/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index c339f61b4e0c3..f463a8f10f7c4 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -12,6 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 build: + noarch: python number: 1 rpaths: - lib/R/lib/ From 7bf46808d452d0a8d1f8ab5656899de97aee0b63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 27 Nov 2018 17:28:39 +0100 Subject: [PATCH 4/5] pin it to python2k --- recipes/bioconductor-dexseq/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index f463a8f10f7c4..1bb84f91c95f0 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -5,18 +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: noarch: python number: 1 rpaths: - lib/R/lib/ - lib/ + requirements: host: - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' @@ -56,16 +59,19 @@ requirements: - r-rcolorbrewer - r-statmod - r-stringr - - python + - python <3 + 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 From a5221f37307a06cf1503df45486398148d474c5b Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 27 Nov 2018 16:18:36 -0500 Subject: [PATCH 5/5] Add htseq requirement, support only python <3 for now --- recipes/bioconductor-dexseq/build.sh | 4 ---- recipes/bioconductor-dexseq/meta.yaml | 1 + 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index 7c45ac75b66b0..e5264766ba3a0 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -5,10 +5,6 @@ $R CMD INSTALL --build . python_scripts=$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' $python_scripts/dexseq_prepare_annotation.py -if [ "$PY3K" == 1 ]; then - 2to3 -w $python_scripts/dexseq_count.py - 2to3 -w $python_scripts/dexseq_prepare_annotation.py -fi chmod +x $python_scripts/dexseq_count.py chmod +x $python_scripts/dexseq_prepare_annotation.py mkdir -p $PREFIX/bin diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 1bb84f91c95f0..ce5855cbc77ba 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -60,6 +60,7 @@ requirements: - r-statmod - r-stringr - python <3 + - 'htseq >=0.9.1' test: commands: