Commit ac7c2e47 authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

execution de scripts sous jenkins : ajout de perl

parent b1391df5
......@@ -10,4 +10,4 @@ ls ${1}
echo "=== remove output data ==="
rm -Rf ${1}/Results
rm -Rf ${1}/log/*
rm -f ${1}/.snakemake
rm -Rf ${1}/.snakemake
......@@ -6,10 +6,14 @@ echo "WORKSPACE=$2"
echo "SNAKEMAKE_JOBS=$3"
export PATH=${1}/miniconda/bin:$PATH
echo $PATH
export LC_ALL=en_US.utf8
export LANG=en_US.utf-8
# Activation of conda virtual environment
echo "=== activate the conda environment ==="
# source activate myVirtualEnv
source activate rnaSeqQuantif
# Configure json environment : Single End or Pair Ends
echo "=== configure the pipeline environement ==="
......
#!/bin/bash
# creation de l'environnement conda
echo $PATH
conda env create -qf -n rnaSeqQuantif snakemake fastqc multiqc cutadapt prinseq star htseq gzip -c bioconda -c conda-forge -c ostrokach
conda create -yq -n rnaSeqQuantif snakemake perl fastqc multiqc cutadapt prinseq star htseq gzip -c bioconda -c conda-forge -c ostrokach
source activate rnaSeqQuantif
conda install bioconductor-deseq2 bioconductor-biomart -c bioconda
conda install -yq bioconductor-deseq2 bioconductor-biomart -c bioconda
source deactivate
......@@ -145,7 +145,7 @@ rule prinseq:
params: preGood = OUTPUTDIR+"/Samples/{sampleName}/PRINSEQ/{sampleName}_{pairNumber}_good",
preBad = OUTPUTDIR+"/Samples/{sampleName}/PRINSEQ/{sampleName}_{pairNumber}_bad"
shell: """
prinseq-lite.pl -min_qual_mean 30 -no_qual_header -fastq {input[0]} -fastq2 {input[1]} -out_good {params.preGood} -out_bad {params.preBad} -log {output.log}
perl `which prinseq-lite.pl` -min_qual_mean 30 -no_qual_header -fastq {input[0]} -fastq2 {input[1]} -out_good {params.preGood} -out_bad {params.preBad} -log {output.log}
if(! test -f {params.preBad}_1.fastq);then touch {params.preBad}_1.fastq {params.preGood}_1_singletons.fastq;fi
if(! test -f {params.preBad}_2.fastq);then touch {params.preBad}_2.fastq {params.preGood}_2_singletons.fastq;fi
"""
......
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