From c13a4f60f50a2f6095e86d26603ccad04527c77c Mon Sep 17 00:00:00 2001 From: cat-bro Date: Fri, 17 Nov 2023 15:42:54 +1100 Subject: [PATCH 1/2] more memory for all bedtools tools --- .../production/total_perspective_vortex/tools.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 9f65ee368..da692c0a4 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 @@ -1065,7 +1065,7 @@ tools: if: input_size < 0.5 cores: 1 mem: 3.8 - toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/.*: + toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools.*: mem: 8 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/.*: scheduling: From 3abc107182a6b38580bb987d92d35b4e4b305398 Mon Sep 17 00:00:00 2001 From: cat-bro Date: Fri, 17 Nov 2023 15:51:01 +1100 Subject: [PATCH 2/2] keep fastqc jobs on local slurm if inputs are over 20GB --- .../production/total_perspective_vortex/tools.yml | 5 +++++ 1 file changed, 5 insertions(+) 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 da692c0a4..627625164 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 @@ -535,6 +535,11 @@ tools: if: 0.01 <= input_size < 2 cores: 4 mem: 15.3 + - id: fastqc_large_input_rule + if: input_size > 20 + scheduling: + require: + - slurm toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/.*: params: singularity_enabled: true