From dabd56ed9fdb3a354ef4290d43ce80c9efd21123 Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Tue, 10 Sep 2024 14:22:32 +1000
Subject: [PATCH] singularity for some GTN tools + all of ecology and galaxyp
 owned tools

For tools PR https://github.com/usegalaxy-au/usegalaxy-au-tools/pull/1130

Set singularity_enabled: true for all tools owned by ecology or galaxyp. For galaxyp there are some exceptions such as msconvert where docker_enabled is true and singularity_enabled is now set to false.
---
 .../total_perspective_vortex/tools.yml        | 21 +++++++++++++++++--
 1 file changed, 19 insertions(+), 2 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 85cef89d1..9ef5311b5 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
@@ -912,6 +912,9 @@ tools:
     - id: scanpy_run_pca_fail_rule
       if: input_size > 20
       fail: Too much data. Total input data must be less than 20GB.
+  toolshed.g2.bx.psu.edu/repos/ecology/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/.*:
     params:
       singularity_enabled: true
@@ -1052,6 +1055,9 @@ tools:
     - id: smudgeplot_fail_rule
       if: input_size > 50
       fail: Too much data. Total input data must be less than 50GB.
+  toolshed.g2.bx.psu.edu/repos/galaxyp/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/.*:
     scheduling:
       accept:
@@ -1076,6 +1082,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/galaxyp/diann/diann/.*:
     params:
       docker_enabled: true
+      singularity_enabled: false
     rules:
     - if: |
         not user or not 'diann' in [role.name for role in user.all_roles() if not role.deleted]
@@ -1120,9 +1127,9 @@ tools:
       - id: maxquant_singularity_rule
         if: |
           minimum_singularity_version = '2.0.3.0+galaxy0'
-          helpers.tool_version_gte(tool, minimum_singularity_version)
+          helpers.tool_version_lt(tool, minimum_singularity_version)
         params:
-          singularity_enabled: true
+          singularity_enabled: false
   toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/.*:
     cores: 16
     mem: 61.4
@@ -1140,6 +1147,7 @@ tools:
     mem: 3.8
     params:
       docker_enabled: true
+      singularity_enabled: false
       tmp_dir: true
   toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/.*:
     mem: 61.4
@@ -1421,6 +1429,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/.*:
     params:
       singularity_enabled: true
@@ -2364,6 +2375,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/.*:
     cores: 3
     mem: 11.5
+  toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/.*:
+    params:
+      singularity_enabled: true  
   toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/.*:
     cores: 8
     mem: 30.7
@@ -2575,6 +2589,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/scater_.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/schicexplorer_.*:
     params:
       singularity_enabled: true