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Update destinations.yml.j2
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removes extra quotes in singularity_run_extra_arguments
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martindemko authored Jan 14, 2025
1 parent 36777aa commit af86eb4
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion files/galaxy/tpv/destinations.yml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -315,7 +315,7 @@ destinations:
jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/staging"
persistence_directory: "/opt/pulsar/files/persistent"
singularity_volumes: "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,$ALPHAFOLD_DB:/data:ro"
singularity_run_extra_arguments: "--nv --env ALPHAFOLD_USE_GPU=True --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR"
singularity_run_extra_arguments: "--nv --env ALPHAFOLD_USE_GPU=True --env SCRATCHDIR=$SCRATCHDIR --env SCRATCH=$SCRATCHDIR"
submit_native_specification: "-l select=1:ncpus=8:mem={int(mem)}gb:scratch_local=100gb:ngpus=1:gpu_mem=16gb -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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