From 21b77711cd49329978377ee58c83704e5c2d47ec Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 19 Sep 2023 15:02:26 +1000 Subject: [PATCH 1/3] Override the container for braker3 --- .../production/total_perspective_vortex/tools.yml | 9 +++++++++ 1 file changed, 9 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 d662d08b7..3a5c6c771 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 @@ -2545,3 +2545,12 @@ tools: - if: | not user or not 'Fgenesh' in [role.name for role in user.all_roles() if not role.deleted] fail: Your account has not been given access to fgenesh. Contact help@genome.edu.au if you think this is in error. + + toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: + mem: 4 + cores: 6 + params: + singularity_container_id_override: docker://teambraker/braker3:v.1.0.4 + scheduling: + require: + - singularity From d374fd15cbc771c8f2ba2b7521f03f5572ea5d5b Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 19 Sep 2023 15:07:40 +1000 Subject: [PATCH 2/3] singularity --- .../production/total_perspective_vortex/tools.yml | 4 +--- 1 file changed, 1 insertion(+), 3 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 3a5c6c771..0782e3fcd 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 @@ -2551,6 +2551,4 @@ tools: cores: 6 params: singularity_container_id_override: docker://teambraker/braker3:v.1.0.4 - scheduling: - require: - - singularity + singularity_enabled: true From 4961ae4ec3fe8ae48ce20bc36bc276dd5ee10d51 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Wed, 20 Sep 2023 13:13:52 +1000 Subject: [PATCH 3/3] braker3 -> test --- jenkins/update_labels/tool_labels.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/jenkins/update_labels/tool_labels.yml b/jenkins/update_labels/tool_labels.yml index 3460fa437..01d27243c 100644 --- a/jenkins/update_labels/tool_labels.yml +++ b/jenkins/update_labels/tool_labels.yml @@ -6,6 +6,8 @@ deprecated: - toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/* - toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/* - toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/* +test: +- toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/* training-only: - toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvet/* - toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/*