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 8973faf61..f7ed2a51e 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_.*: @@ -714,7 +714,7 @@ 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 @@ -759,7 +759,7 @@ 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: | @@ -773,7 +773,7 @@ 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 @@ -797,7 +797,7 @@ 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: | @@ -1051,7 +1051,7 @@ 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/.*: @@ -1084,7 +1084,7 @@ 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: @@ -1154,10 +1154,10 @@ 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 @@ -1172,7 +1172,7 @@ 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 @@ -1193,7 +1193,7 @@ 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 @@ -1640,7 +1640,7 @@ 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: @@ -1714,7 +1714,7 @@ 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 @@ -1818,7 +1818,7 @@ 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 @@ -1937,7 +1937,7 @@ 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: @@ -1977,10 +1977,10 @@ 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 @@ -2348,7 +2348,7 @@ 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: @@ -2462,7 +2462,7 @@ 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 @@ -2494,7 +2494,7 @@ 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 @@ -2511,7 +2511,7 @@ 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 @@ -2689,7 +2689,7 @@ 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 @@ -2909,8 +2909,8 @@ 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 @@ -2919,13 +2919,13 @@ 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 @@ -2940,7 +2940,7 @@ 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 @@ -3060,7 +3060,7 @@ 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 @@ -3244,7 +3244,7 @@ tools: context: max_concurrent_job_count_for_tool_user: 3 cores: 16 - mem: 61.4 + mem: 62 params: singularity_enabled: true tmp_dir: true @@ -3403,10 +3403,10 @@ 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 @@ -3444,13 +3444,13 @@ 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: