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fixes error with incorrectly used brackets (3.0)
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martindemko committed Jul 31, 2024
1 parent eb47607 commit b7f0b42
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion files/galaxy/tpv/destinations.yml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,8 @@ destinations:
jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/staging"
persistence_directory: "/opt/pulsar/files/persistent"
singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro"
singularity_run_extra_arguments: '--env _JAVA_OPTIONS=\"-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR\"'
singularity_env__JAVA_OPTIONS: '"-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"'
# singularity_run_extra_arguments: '--env _JAVA_OPTIONS=\"-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR\"'
submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb -l walltime=24:00:00 -q [email protected] -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
scheduling:
require:
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