From 907a5238216553df64a541e9e1456ebd6434ccf3 Mon Sep 17 00:00:00 2001 From: rlibouban Date: Wed, 31 Jan 2024 15:19:04 +0100 Subject: [PATCH 1/4] small modifications --- files/galaxy/tpv/tools.yml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index a6d745b3c..e7e70f3e6 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1060,21 +1060,21 @@ tools: require: - singularity - toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.6.*: + toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: + cores : 6 mem: 4 - cores: 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/" - - toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.3.*: - mem: 4 - cores: 6 params: - singularity_container_id_override: docker://quay.io/bgruening/braker3:v.1.0.4 - scheduling: - require: - - singularity + singularity_enabled: true + rules: + - if: helpers.tool_version_eq(tool, '3.0.3'): + params: + singularity_container_id_override: docker://teambraker/braker3:v.1.0.4 + - if: helpers.tool_version_eq(tool, '3.0.6'): + params: + singularity_container_id_override: docker://teambraker/braker3:v1.0.6 + - if: helpers.tool_version_eq(tool, '3.0.7'): + params: + singularity_container_id_override: docker://teambraker/braker3:v3.0.7.1 # GeneMark is a pain and needs special casing toolshed.g2.bx.psu.edu/repos/genouest/braker/braker/.*: From 6d1235ac3e47d06698cb19531fdb47ccd7c6124c Mon Sep 17 00:00:00 2001 From: rlibouban Date: Wed, 31 Jan 2024 15:30:45 +0100 Subject: [PATCH 2/4] small modifications --- files/galaxy/tpv/tools.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index e7e70f3e6..17d540418 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1061,20 +1061,20 @@ tools: - singularity toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: - cores : 6 + cores: 6 mem: 4 params: - singularity_enabled: true + singularity_enabled: true rules: - if: helpers.tool_version_eq(tool, '3.0.3'): - params: - singularity_container_id_override: docker://teambraker/braker3:v.1.0.4 + execute: | + entity.params['singularity_container_id_override']: docker://teambraker/braker3:v.1.0.4 - if: helpers.tool_version_eq(tool, '3.0.6'): - params: - singularity_container_id_override: docker://teambraker/braker3:v1.0.6 + execute: | + entity.params['singularity_container_id_override']: docker://teambraker/braker3:v1.0.6 - if: helpers.tool_version_eq(tool, '3.0.7'): - params: - singularity_container_id_override: docker://teambraker/braker3:v3.0.7.1 + execute: | + entity.params['singularity_container_id_override']: docker://teambraker/braker3:v3.0.7.1 # GeneMark is a pain and needs special casing toolshed.g2.bx.psu.edu/repos/genouest/braker/braker/.*: From 96095556fd8f694d72ebc0ca1ac38abecfca5953 Mon Sep 17 00:00:00 2001 From: rlibouban Date: Wed, 31 Jan 2024 15:33:27 +0100 Subject: [PATCH 3/4] small modifications --- files/galaxy/tpv/tools.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 17d540418..9f6984a2f 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1068,13 +1068,13 @@ tools: rules: - if: helpers.tool_version_eq(tool, '3.0.3'): execute: | - entity.params['singularity_container_id_override']: docker://teambraker/braker3:v.1.0.4 + entity.params['singularity_container_id_override']="docker://teambraker/braker3:v.1.0.4" - if: helpers.tool_version_eq(tool, '3.0.6'): execute: | - entity.params['singularity_container_id_override']: docker://teambraker/braker3:v1.0.6 + entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6" - if: helpers.tool_version_eq(tool, '3.0.7'): execute: | - entity.params['singularity_container_id_override']: docker://teambraker/braker3:v3.0.7.1 + entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1" # GeneMark is a pain and needs special casing toolshed.g2.bx.psu.edu/repos/genouest/braker/braker/.*: From 041ebe3067d7df1fa9a59be081ced5c1dbe9d0f5 Mon Sep 17 00:00:00 2001 From: rlibouban Date: Wed, 31 Jan 2024 15:34:55 +0100 Subject: [PATCH 4/4] small modifications --- files/galaxy/tpv/tools.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 9f6984a2f..48e88858d 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -1066,13 +1066,13 @@ tools: params: singularity_enabled: true rules: - - if: helpers.tool_version_eq(tool, '3.0.3'): + - if: helpers.tool_version_eq(tool, '3.0.3') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v.1.0.4" - - if: helpers.tool_version_eq(tool, '3.0.6'): + - if: helpers.tool_version_eq(tool, '3.0.6') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6" - - if: helpers.tool_version_eq(tool, '3.0.7'): + - if: helpers.tool_version_eq(tool, '3.0.7') execute: | entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1"