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reject docker and unify tpv configs #194
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cf6a54a
seperate tpv rules into proper local files
martenson f28bc21
update some ids to full path
martenson 6736b3b
wip tpv and local tools
martenson 6172ae5
hide tools removed from distribution
martenson 8cf0398
update tool_panel confs
martenson e666168
move nasty java back to meta tpv rules
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -44,6 +44,6 @@ tools: | |
| mem: 16 | ||
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| .*/fastqc/.*: | ||
| cores: 1 | ||
| cores: 1 | ||
| context: | ||
| walltime: 2 | ||
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1 change: 0 additions & 1 deletion
1
...laxy.cloud.e-infra.cz/tpv_rules_local.yml → files/galaxy/config/tpv_rules_local.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,2 @@ | ||
| # prevent tpv lint complaints | ||
| global: | ||
| default_inherits: default |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,70 @@ | ||
| global: | ||
| default_inherits: default | ||
| destinations: | ||
| tpv_pulsar_rosettafold: | ||
| inherits: tpv_pulsar | ||
| 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'}" | ||
| scheduling: | ||
| require: | ||
| - rosettafold | ||
| tpv_pulsar_rosettafold_sing: | ||
| inherits: tpv_pulsar_rosettafold | ||
| container_resolvers: | ||
| - type: explicit_singularity | ||
| - cache_directory: /cvmfs/singularity.metacentrum.cz/RoseTTAFold2/ | ||
| type: cached_mulled_singularity | ||
| params: | ||
| singularity_enabled: true | ||
| singularity_run_extra_arguments: '--nv --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR' | ||
| singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' | ||
| singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" | ||
| scheduling: | ||
| require: | ||
| - singularity | ||
| tpv_pulsar_alphafold: | ||
| inherits: tpv_pulsar | ||
| max_accepted_gpus: 1 | ||
| max_gpus: 1 | ||
| runner: pulsar_tpv_runner | ||
| params: | ||
| singularity_run_extra_arguments: '--nv' | ||
| singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' | ||
| submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" | ||
| scheduling: | ||
| require: | ||
| - alphafold | ||
| tools: | ||
| testing_rosettafold2: | ||
| cores: 8 | ||
| mem: 64 | ||
| gpus: 1 | ||
| context: | ||
| walltime: 24 | ||
| scratch: 25 | ||
| gpu_mem: 16 | ||
| scheduling: | ||
| require: | ||
| - rosettafold | ||
| rosettafold2: | ||
| inherits: testing_rosettafold2 | ||
| scheduling: | ||
| require: | ||
| - singularity | ||
| toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*: | ||
| cores: 8 | ||
| mem: 120 | ||
| gpus: 1 | ||
| context: | ||
| walltime: 24 | ||
| scratch: 100 | ||
| gpu_mem: 16 | ||
| env: | ||
| MPLCONFIGDIR: "$SCRATCHDIR" | ||
| ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db" | ||
| ALPHAFOLD_USE_GPU: True | ||
| scheduling: | ||
| require: | ||
| - alphafold | ||
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