From bfd3ee63a2f9ab7e44fa269a910941bf9713fb7f Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Fri, 2 Feb 2024 12:33:19 +0000 Subject: [PATCH 1/2] Add Germark env to braker3 version 3.0.6 It got mistakenly removed in the PR https://github.com/usegalaxy-eu/infrastructure-playbook/pull/1091 --- files/galaxy/tpv/tools.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index dd5919bff..6e0de7193 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1072,6 +1072,9 @@ tools: - if: helpers.tool_version_eq(tool, '3.0.6+galaxy2') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6" + env: + GENEMARK_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/" + PROTHINT_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/gmes/ProtHint/bin/" - if: helpers.tool_version_eq(tool, '3.0.7+galaxy2') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1" From 56b11c81c050229fc7cdee606aa01557e35405ff Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Fri, 2 Feb 2024 12:41:35 +0000 Subject: [PATCH 2/2] Fix trailing spaces lint error --- files/galaxy/tpv/tools.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 6e0de7193..097ae1559 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1074,7 +1074,7 @@ tools: entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6" env: GENEMARK_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/" - PROTHINT_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/gmes/ProtHint/bin/" + PROTHINT_PATH: "/usr/local/tools/_conda/envs/__braker3@3.0.6/bin/genemark/bin/gmes/ProtHint/bin/" - if: helpers.tool_version_eq(tool, '3.0.7+galaxy2') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1"