From 6e42d09ef468cb54ae9fc81898f5a00523da66c3 Mon Sep 17 00:00:00 2001 From: cat-bro Date: Tue, 17 Sep 2024 14:32:33 +1000 Subject: [PATCH] Add _JAVA_OPTIONS env vars to bbtools --- .../production/total_perspective_vortex/tools.yml | 3 +++ 1 file changed, 3 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 8040a41bd..511a05585 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 @@ -1293,6 +1293,9 @@ tools: cores: 1 mem: 3.8 toolshed.g2.bx.psu.edu/repos/iuc/bbtools_.*: + env: + SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G + _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G params: singularity_enabled: true toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/.*: