Commit 790dba35 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

activate specific conda env when present in yaml file

parent 07b7a2e4
......@@ -59,6 +59,11 @@ grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | xargs dirname | x
# Download run files from iRODS
grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | awk '{print "java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar --pull --local "$1" --files "$1" --force"}' | sh
# Start a conda environment when needed
conda_env=`grep conda $yaml | awk -F": " '{print $2}'`
if ! [[ -z "$conda" ]]; then
source /root/miniconda/bin/activate && conda activate $conda_env
# Run workflow with or without provenance
if $prov; then
cwltool --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path --provenance $destination_path/PROVENANCE $cwl $yaml
......
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