Commit 7c82506d authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

run.sh update to allow multiple downloads in a one liner

parent 350a0b61
......@@ -63,9 +63,10 @@ java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar -pull --files
destination_path=`cat $yaml | grep destination | awk -F": " '{print $2}'`
# Create parent folders to store the files in
grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | xargs dirname | xargs mkdir -p
# grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | xargs dirname | xargs mkdir -p
# 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}' | sh
grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | tr '\n' ' ' | awk '{print "java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar --preserve --pull --local / --files "$0}'
grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | tr '\n' ' ' | awk '{print "java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar --preserve --pull --local / --files "$0}' | sh
# Run workflow with or without provenance
if $prov; then
......@@ -100,7 +101,7 @@ if [ $exit_status -eq 0 ]; then
echo removing $destination_path/CACHE_$yaml_file_name
rm -r $destination_path/CACHE_$yaml_file_name
# Upload the provenance $4=Final destination (Hash path)
# Upload the provenance
java -jar /unlock/infrastructure/binaries/irods/IRODSTransfer.jar --push --files $destination_path --irods $destination_path
# Update metadata field
......
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