diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2 index 6915e911f..29913be4a 100644 --- a/files/galaxy/tpv/destinations.yml.j2 +++ b/files/galaxy/tpv/destinations.yml.j2 @@ -259,7 +259,7 @@ 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,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro" - singularity_env__JAVA_OPTIONS: '"-Xmx{int(mem)}g -Djava.io.tmpdir=$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 galaxyeu@pbs-m1.metacentrum.cz -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: