Commit 43008d7c authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

conda is now installed in workspace, to allow concurrent pipeline execution

parent c5bfb91b
#!/bin/bash
# usage : bash executePipeline.sh JENKSINS_HOME WORKSPACE SNAKEMAKE_JOBS
# usage : bash executePipeline.sh WORKSPACE SNAKEMAKE_JOBS
echo "JENKINS_HOME=$1"
echo "WORKSPACE=$2"
echo "SNAKEMAKE_JOBS=$3"
......@@ -22,7 +21,7 @@ echo "=== configure the pipeline environement ==="
# 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"
snakemake -rp --jobs ${2} --config projf="CONFIG/project.json" reff="CONFIG/references.json" conff="CONFIG/config.json"
# check the result
echo "=== check the result ==="
......
#!/bin/bash
# usage : bash scripts/setupConda.sh JENKINS_HOME JENKINS_WORKSPACE
# usage : bash scripts/setupConda.sh JENKINS_WORKSPACE
# change directory to Jenkins home
cd ${1}
# list directory contents for the Jenkins worskspace directory
ls -al ${1}
# remove conda environments
echo "=== remove conda environments ==="
......@@ -20,7 +20,7 @@ rm -f ${1}/miniconda.sh
export PATH=${1}/miniconda/bin:$PATH
# Install of the exome environment
/bin/bash ${2}/CONDA/createEnv.sh
/bin/bash ${1}/CONDA/createEnv.sh
# List environment
echo "=== list available conda environments ==="
......
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