From 18339f9d122350416ef37d6817e191928ab34856 Mon Sep 17 00:00:00 2001 From: cat-bro Date: Mon, 7 Oct 2024 13:43:37 +1100 Subject: [PATCH] stacks denovomap memory --- .../total_perspective_vortex/tools.yml | 72 +++++++++---------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml index 1080be40..a6318aac 100644 --- a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml +++ b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml @@ -12,10 +12,10 @@ tools: mem: 7.6 testtoolshed.g2.bx.psu.edu/repos/simon-gladman/phyloseq_filter/biom_filter/.*: cores: 16 - mem: 61.4 + mem: 62 testtoolshed.g2.bx.psu.edu/repos/simon-gladman/phyloseq_ordination_plot/phyloseq_ordinate/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/.*: mem: 12 toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*: @@ -85,7 +85,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/.*: cores: 16 - mem: 61.4 + mem: 62 params: docker_enabled: true toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_.*: @@ -718,7 +718,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/.*: cores: 16 - mem: 61.4 + mem: 62 scheduling: accept: - pulsar @@ -763,7 +763,7 @@ tools: - pulsar toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/.*: cores: 16 - mem: 61.4 + mem: 62 rules: - id: ncbi_blastx_wrapper_pulsar_rule if: | @@ -777,7 +777,7 @@ tools: - pulsar toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/.*: cores: 16 - mem: 61.4 + mem: 62 rules: - id: ncbi_makeblastdb_small_input_rule if: input_size < 30 @@ -801,7 +801,7 @@ tools: - pulsar toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/.*: cores: 16 - mem: 61.4 + mem: 62 rules: - id: ncbi_tblastx_wrapper_pulsar_rule if: | @@ -1055,7 +1055,7 @@ tools: - slurm toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*: cores: 16 - mem: 61.4 + mem: 62 params: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/galaxy-australia/metawrapmg_binning/metawrapmg_binning/.*: @@ -1088,7 +1088,7 @@ tools: accept: - pulsar toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/.*: - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/.*: scheduling: accept: @@ -1158,10 +1158,10 @@ tools: singularity_enabled: false toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant_mqpar/maxquant_mqpar/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/galaxyp/morpheus/morpheus/.*: params: singularity_enabled: true @@ -1176,7 +1176,7 @@ tools: singularity_enabled: false tmp_dir: true toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/.*: - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/.*: cores: 7 mem: 26.8 @@ -1197,7 +1197,7 @@ tools: mem: 8 toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: cores: 16 - mem: 61.4 + mem: 62 params: singularity_container_id_override: docker://teambraker/braker3:v1.0.6 singularity_enabled: true @@ -1641,7 +1641,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/.*: cores: 16 - mem: 61.4 + mem: 62 params: singularity_enabled: true scheduling: @@ -1715,7 +1715,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/iuc/hyphy_absrel/hyphy_absrel/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/hyphy_gard/hyphy_gard/.*: cores: 20 mem: 200 @@ -1819,7 +1819,7 @@ tools: - id: khmer_abundance_distribution_single_medium_input_rule if: 0.1 <= input_size < 0.5 cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/kraken.*: params: singularity_enabled: true @@ -1938,7 +1938,7 @@ tools: context: max_concurrent_job_count_for_tool_user: 2 # TODO: this tool could go to high memory pulsars instead cores: 16 - mem: 61.4 + mem: 62 params: singularity_enabled: true scheduling: @@ -1978,10 +1978,10 @@ tools: - id: meryl_medium_input_rule if: 0.001 <= input_size < 5 cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/.*: cores: 16 - mem: 61.4 + mem: 62 rules: - id: metaphlan_small_input_rule if: input_size < 0.001 @@ -2349,7 +2349,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/.*: cores: 16 - mem: 61.4 + mem: 62 env: _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G scheduling: @@ -2460,7 +2460,7 @@ tools: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: cores: 16 - mem: 61.4 + mem: 62 rules: - id: quast_small_input_rule if: input_size < 1 @@ -2492,7 +2492,7 @@ tools: - id: raven_medium_input_rule if: 0.002 <= input_size < 5 cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/.*: cores: 24 mem: 250 @@ -2509,7 +2509,7 @@ tools: - id: raxml_medium_input_rule if: 0.0005 <= input_size < 0.1 cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/.*: params: singularity_enabled: true @@ -2687,7 +2687,7 @@ tools: - id: shasta_medium_input_rule if: 0.002 <= input_size < 5 cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*: cores: 10 mem: 38.3 @@ -2907,8 +2907,8 @@ tools: cores: 3 mem: 11.5 toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/.*: - cores: 4 - mem: 16 + cores: 16 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/stacks2.*: params: singularity_enabled: true @@ -2917,13 +2917,13 @@ tools: mem: 7.6 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_denovomap/stacks2_denovomap/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_kmerfilter/stacks2_kmerfilter/.*: cores: 2 mem: 7.6 @@ -2938,7 +2938,7 @@ tools: mem: 7.6 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/.*: cores: 16 - mem: 61.4 + mem: 62 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/.*: cores: 8 mem: 42 @@ -3058,7 +3058,7 @@ tools: mem: 19.1 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_consensus/trycycler_consensus/.*: cores: 16 - mem: 61.4 + mem: 62 scheduling: accept: - pulsar @@ -3242,7 +3242,7 @@ tools: context: max_concurrent_job_count_for_tool_user: 3 cores: 16 - mem: 61.4 + mem: 62 params: singularity_enabled: true tmp_dir: true @@ -3398,10 +3398,10 @@ tools: mem: 3.8 .*bowtie2_index_builder_data_manager.*: cores: 16 - mem: 61.4 + mem: 62 .*bwa_mem_index_builder_data_manager.*: cores: 16 - mem: 61.4 + mem: 62 .*bwameth_index_builder_data_manager.*: cores: 5 mem: 19.1 @@ -3439,13 +3439,13 @@ tools: mem: 19.1 .*kraken2_build_database.*: cores: 16 - mem: 61.4 + mem: 62 .*rna_star_index_builder_data_manager.*: cores: 32 mem: 122.8 .*twobit_builder_data_manager.*: cores: 16 - mem: 61.4 + mem: 62 'Convert characters1': mem: 8 Cut1: