Commit 48449711 authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

script d'exécution

parent fc8cc912
#!/bin/bash
# usage : bash executePipeline.sh JENKSINS_HOME WORKSPACE SNAKEMAKE_JOBS
echo "JENKINS_HOME=$1"
echo "WORKSPACE=$2"
echo "SNAKEMAKE_JOBS=$3"
export PATH=${1}/miniconda/bin:$PATH
# Activation of conda virtual environment
echo "=== activate the conda environment ==="
# source activate myVirtualEnv
# Configure json environment : Single End or Pair Ends
echo "=== configure the pipeline environement ==="
# cp myConfig.json config.json
# Run pipeline
echo "=== run the pipeline ==="
echo "number of snakemake jobs : $SNAKEMAKE_JOBS"
snakemake -rp --jobs ${3} --config projf="CONFIG/project.json" reff="CONFIG/references.json" conff="CONFIG/config.json"
# check the result
echo "=== check the result ==="
export checksum="89c0a3d1cc26f67c5262c0f6b7a6f341"
export checksum_ref="89c0a3d1cc26f67c5262c0f6b7a6f341"
if [[ "$checksum" == "$checksum_ref" ]]; then
echo "succes"
else
echo "failure"
echo "checksum = $checksum"
echo "checksum_ref = $checksum_ref"
# exit 1
fi
# Desactivation of the conda virtual environment
echo "=== deactivate the conda environment ==="
source deactivate
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