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Singularity update 20231024 1 #1582

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merged 2 commits into from
Oct 24, 2023
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Singularity update 20231024 1 #1582

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117ab54
wip
cat-bro Oct 10, 2023
503cb4d
Remove inheritance so spades tools can have their own singularity par…
cat-bro Oct 24, 2023
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124 changes: 119 additions & 5 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 @@ -1172,6 +1172,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/.*:
cores: 16
mem: 61.4
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
Expand Down Expand Up @@ -1723,6 +1725,9 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/.*:
cores: 3
mem: 11.5
toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/.*:
params:
singularity_enabled: true
Expand Down Expand Up @@ -1955,6 +1960,8 @@ tools:
accept:
- pulsar
- pulsar-training-large
params:
singularity_enabled: true
rules:
- id: rnaspades_small_input_rule
if: input_size < 0.005
Expand Down Expand Up @@ -2105,18 +2112,114 @@ tools:
cores: 3
mem: 11.5
toolshed.g2.bx.psu.edu/repos/iuc/spades_biosyntheticspades/spades_biosyntheticspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
cores: 20
mem: 500
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
- pulsar-training-large
rules:
- id: spades_biosyntheticspades_small_input_rule
if: input_size < 0.005
cores: 2
mem: 7.6
- id: spades_biosyntheticspades_medium_input_rule
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- id: spades_biosyntheticspades_fail_rule
if: input_size >= 20
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_coronaspades/spades_coronaspades/.*:
cores: 20
mem: 500
scheduling:
accept:
- pulsar-paw
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
- pulsar
- pulsar-training-large
rules:
- if: |
minimum_singularity_version = '3.15.4+galaxy0'
helpers.tool_version_gte(tool, minimum_singularity_version)
params:
singularity_enabled: true
- id: spades_coronaspades_small_input_rule
if: input_size < 0.005
cores: 2
mem: 7.6
- id: spades_coronaspades_medium_input_rule
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- id: spades_coronaspades_fail_rule
if: input_size >= 20
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaplasmidspades/spades_metaplasmidspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
cores: 20
mem: 500
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
- pulsar-training-large
rules:
- id: spades_metaplasmidspades_small_input_rule
if: input_size < 0.005
cores: 2
mem: 7.6
- id: spades_metaplasmidspades_medium_input_rule
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- id: spades_metaplasmidspades_fail_rule
if: input_size >= 20
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
cores: 20
mem: 500
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
- pulsar-training-large
rules:
- id: spades_metaviralspades_small_input_rule
if: input_size < 0.005
cores: 2
mem: 7.6
- id: spades_metaviralspades_medium_input_rule
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- id: spades_metaviralspades_fail_rule
if: input_size >= 20
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
cores: 20
mem: 500
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
- pulsar-training-large
rules:
- id: spades_plasmidspades_small_input_rule
if: input_size < 0.005
cores: 2
mem: 7.6
- id: spades_plasmidspades_medium_input_rule
if: 0.005 <= input_size < 2
cores: 8
mem: 30.7
- id: spades_plasmidspades_fail_rule
if: input_size >= 20
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/iuc/spades_rnaviralspades/spades_rnaviralspades/.*:
cores: 10
mem: 250
Expand All @@ -2125,6 +2228,11 @@ tools:
- pulsar
- pulsar-training-large
rules:
- if: |
minimum_singularity_version = '3.15.4+galaxy1'
helpers.tool_version_gte(tool, minimum_singularity_version)
params:
singularity_enabled: true
- id: spades_rnaviralspades_small_input_rule
if: input_size < 0.005
cores: 2
Expand Down Expand Up @@ -2413,6 +2521,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/.*:
cores: 16
mem: 61.4
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
Expand All @@ -2432,6 +2542,8 @@ tools:
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*:
cores: 20
mem: 500
params:
singularity_enabled: true
scheduling:
accept:
- pulsar
Expand Down Expand Up @@ -2535,6 +2647,8 @@ tools:
cores: 1
mem: 3.8
toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/.*:
params:
singularity_enabled: true
cores: 3
mem: 11.5
.*bowtie2_index_builder_data_manager.*:
Expand Down
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