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Fixes cases when tool ID includes spaces #334

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Fixes cases when tool ID includes spaces #334

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26e1fcf
Fixes cases when tool ID includes spaces
martindemko Jun 17, 2026
8cb2e0b
fixes more submit_native_specification in TPV config
martindemko Jun 18, 2026
9614580
rearranges submit_native_specifications in TPV config
martindemko Jun 18, 2026
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25 changes: 21 additions & 4 deletions templates/galaxy/config/tpv_rules_meta.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,11 @@ destinations:
ssh_key: |
{{ pulsar_ssh_key | indent(width=8,first=False) }}
outputs_to_working_directory: false
submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_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'}"
submit_native_specification: >-
-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb
-l walltime={int(walltime)}:00:00
-q {queue}
-N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
env:
TMPDIR: $SCRATCHDIR
TMP: $SCRATCHDIR
Expand Down Expand Up @@ -401,7 +405,12 @@ destinations:
inherits: tpv_pulsar
runner: pulsar_tpv_runner
params:
submit_native_specification: "-l place=exclhost -l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N pulsar-re_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'}"
submit_native_specification: >-
-l place=exclhost
-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb
-l walltime={int(walltime)}:00:00
-q {queue}
-N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
scheduling:
require:
- exclusive
Expand All @@ -426,7 +435,11 @@ destinations:
runner: pulsar_tpv_runner
params:
singularity_enabled: false
submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_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'}"
submit_native_specification: >-
-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb
-l walltime={int(walltime)}:00:00
-q {{ pulsar.pbs_gpu_queue }}
-N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
scheduling:
require:
- rosettafold
Expand All @@ -452,7 +465,11 @@ destinations:
params:
singularity_run_extra_arguments: '--nv'
singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro'
submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_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'}"
submit_native_specification: >-
-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb
-l walltime={int(walltime)}:00:00
-q {{ pulsar.pbs_gpu_queue }}
-N {{ pulsar.nfs_prefix }}_j{job.id}__{(tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]).replace(' ','_')}__{user.username if user and hasattr(user, 'username') else 'anonymous'}
scheduling:
require:
- alphafold