From 3993b0df84a86daba0b796411f8f28b4f8b2687e Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Mon, 13 May 2024 10:11:44 +0200 Subject: [PATCH] never trust the linter --- files/galaxy/tpv/tools.yml | 40 +++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 9d4025cdf..a986a844e 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -22,17 +22,17 @@ tools: - id: no-pulsar if: user is not None execute: | - from tpv.core.entities import Tag, TagSetManager, TagType + from tpv.core.entities import Tag, TagSetManager, TagType - user_preferences = user.extra_preferences - pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None") - pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None + user_preferences = user.extra_preferences + pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None") + pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None - entity.tpv_tags.tags = [ - tag - for tag in entity.tpv_tags.tags - if tag != pulsar_tag - ] + entity.tpv_tags.tags = [ + tag + for tag in entity.tpv_tags.tags + if tag != pulsar_tag + ] env: TEMP: /data/1/galaxy_db/tmp @@ -282,13 +282,13 @@ tools: params: singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases/2.3/,ALPHAFOLD_USE_GPU=False" - if: helpers.tool_version_gte(tool, '2.3.1+galaxy2') - params: - singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False" execute: | from random import SystemRandom if SystemRandom().random() < 0.10: - entity.gpus = 1 - entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=True' + entity.gpus = 1 + entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=True' + else: + entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False" # tweak amount of requested memory depending on the AlphaFold model to be run - id: model_preset_multimer if: job.get_param_values(app).get("model_preset") == "multimer" @@ -341,7 +341,7 @@ tools: cores: 1 mem: 30 params: - docker_run_extra_arguments: ' --gpus all ' + docker_run_extra_arguments: " --gpus all " env: GPU_AVAILABLE: 1 toolshed.g2.bx.psu.edu/repos/bgruening/whisper/whisper/.*: @@ -715,7 +715,7 @@ tools: mem: 30 gpus: 1 params: - singularity_run_extra_arguments: ' --nv ' + singularity_run_extra_arguments: " --nv " scheduling: require: - singularity @@ -852,7 +852,7 @@ tools: Too much data, we cannot support such large Trinity assemblies with our backend. Please use another server for your job. - '.*mothur_.*': + ".*mothur_.*": cores: 1 mem: 90 params: @@ -865,7 +865,7 @@ tools: # see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421 ##- embedded-pulsar - '.*mothur_classify_seqs.*': + ".*mothur_classify_seqs.*": cores: 2 mem: 20 params: @@ -878,7 +878,7 @@ tools: # see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421 ##- embedded-pulsar - '.*bioext_bam2msa.*': + ".*bioext_bam2msa.*": params: docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" @@ -888,7 +888,7 @@ tools: - docker - embedded-pulsar - 'last_*': + "last_*": params: docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" @@ -964,7 +964,7 @@ tools: require: - singularity - conda -# Not for Pulsar, or is the file copied? + # Not for Pulsar, or is the file copied? toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/.*: env: COPERNICUS_CDSAPIRC_KEY_FILE: /data/db/data_managers/COPERNICUS_CDSAPIRC_KEY_FILE