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Sync job file template with galaxy #350

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merged 5 commits into from
Jan 4, 2024
Merged

Sync job file template with galaxy #350

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be568cf
Sync job file template with galaxy
mvdbeek Dec 14, 2023
4ae378c
Bump up python versions in testing
mvdbeek Dec 14, 2023
a5983e9
Test a tool that's still installable
mvdbeek Dec 14, 2023
bfcea2b
Remove test against cat1 that will always fail
mvdbeek Dec 14, 2023
df11ea1
Write markdown test output to step summary
mvdbeek Dec 14, 2023
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14 changes: 14 additions & 0 deletions pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,20 @@ 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}"

GALAXY_PYTHON=`command -v python`
cd $working_directory
$memory_statement
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