Unverified Commit efef30d6 authored by Matthias Bernt's avatar Matthias Bernt Committed by mvdbeek
Browse files

make sure that TMP, TEMP, and TMPDIR are set 

seems needed for docker volume strings (an empty
variable would lead to `-v "::rw"` which causes
`docker: invalid spec: ::rw: empty section between colons.`)
parent e93e986a

lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh

+23 −0
Original line number Diff line number Diff line
@@ -35,6 +35,29 @@ GALAXY_LIB="$galaxy_lib" 
_galaxy_setup_environment "$PRESERVE_GALAXY_ENVIRONMENT"

export _GALAXY_JOB_HOME_DIR

export _GALAXY_JOB_TMP_DIR



TEMP="${TEMP:-$TMP}"

TMPDIR="${TMPDIR:-$TMP}"



TMP="${TMP:-$TEMP}"

TMPDIR="${TMPDIR:-$TEMP}"



TMP="${TMP:-$TMPDIR}"

TEMP="${TEMP:-$TMPDIR}"



TMP="${TMP:-_GALAXY_JOB_TMP_DIR}"

TEMP="${TEMP:-_GALAXY_JOB_TMP_DIR}"

TMPDIR="${TMPDIR:-_GALAXY_JOB_TMP_DIR}"



export TMP

export TEMP

export TMPDIR



echo "_GALAXY_JOB_TMP_DIR $_GALAXY_JOB_TMP_DIR" >> outputs/tmp 

echo "TMP $TMP" >> outputs/tmp

echo "TEMP $TEMP" >> outputs/tmp 

echo "TMPDIR $TMPDIR" >> outputs/tmp 



GALAXY_PYTHON=`command -v python`

cd $working_directory

$memory_statement