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singularity for some GTN tools + all of ecology and galaxyp owned tools #2155

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Sep 10, 2024
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singularity for some GTN tools + all of ecology and galaxyp owned tools #2155

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21 changes: 19 additions & 2 deletions files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -912,6 +912,9 @@ tools:
- id: scanpy_run_pca_fail_rule
if: input_size > 20
fail: Too much data. Total input data must be less than 20GB.
toolshed.g2.bx.psu.edu/repos/ecology/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/.*:
params:
singularity_enabled: true
Expand Down Expand Up @@ -1052,6 +1055,9 @@ tools:
- id: smudgeplot_fail_rule
if: input_size > 50
fail: Too much data. Total input data must be less than 50GB.
toolshed.g2.bx.psu.edu/repos/galaxyp/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/.*:
scheduling:
accept:
Expand All @@ -1076,6 +1082,7 @@ tools:
toolshed.g2.bx.psu.edu/repos/galaxyp/diann/diann/.*:
params:
docker_enabled: true
singularity_enabled: false
rules:
- if: |
not user or not 'diann' in [role.name for role in user.all_roles() if not role.deleted]
Expand Down Expand Up @@ -1120,9 +1127,9 @@ tools:
- id: maxquant_singularity_rule
if: |
minimum_singularity_version = '2.0.3.0+galaxy0'
helpers.tool_version_gte(tool, minimum_singularity_version)
helpers.tool_version_lt(tool, minimum_singularity_version)
params:
singularity_enabled: true
singularity_enabled: false
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/.*:
cores: 16
mem: 61.4
Expand All @@ -1140,6 +1147,7 @@ tools:
mem: 3.8
params:
docker_enabled: true
singularity_enabled: false
tmp_dir: true
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/.*:
mem: 61.4
Expand Down Expand Up @@ -1421,6 +1429,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/.*:
params:
singularity_enabled: true
Expand Down Expand Up @@ -2364,6 +2375,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/.*:
cores: 3
mem: 11.5
toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/.*:
cores: 8
mem: 30.7
Expand Down Expand Up @@ -2575,6 +2589,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/scater_.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/schicexplorer_.*:
params:
singularity_enabled: true
Expand Down
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