Commit ecf5f312 authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

split conda environment

parent 26d07921
......@@ -12,7 +12,7 @@ rm -Rf ${1}/.continuum
rm -Rf ${1}/miniconda
# Download miniconda
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ${1}/miniconda.sh
/bin/bash ${1}/miniconda.sh -b -p ${1}/miniconda
rm -f ${1}/miniconda.sh
......
......@@ -2,8 +2,6 @@
# creation de l'environnement conda
echo $PATH
conda create -yq -n rnaSeqQuantif bioconductor-deseq2 bioconductor-biomart -c bioconda
conda create -yq -n deseq2 bioconductor-deseq2 bioconductor-biomart -c bioconda
source activate rnaSeqQuantif
conda install -yq snakemake perl fastqc multiqc cutadapt prinseq star htseq gzip ncurses -c bioconda -c conda-forge -c ostrokach
source deactivate
conda create -yq -n rnaSeqQuantif snakemake perl openjdk>8.0.121 fastqc multiqc cutadapt prinseq star htseq gzip ncurses -c bioconda -c conda-forge -c ostrokach
......@@ -240,6 +240,8 @@ rule deseq2:
counts=expand(OUTPUTDIR+"/DESEQ2/counts/{sampleName}",sampleName=sample_all)
output: expand(OUTPUTDIR+"/DESEQ2/results/{suffixe}",suffixe=["NormalizedCountMatrix.txt","NormalizedCountMatrixFiltered.txt","PCAplot.png","sampletosampledistance.jpeg"])
shell: """
source deactivate
source activate deseq2
cat {SCRIPTPATH}/run_deseq2.R | R --slave --args {input.conditions} {OUTPUTDIR}/DESEQ2/counts {OUTPUTDIR}/DESEQ2/results {BIOMART}
"""
......
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