Merge pull request #133 from martenson/regalaxy

automate regalaxy toolset management

Author: martenson

.github/workflows/cron_update.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        instance: [usegalaxy.cz, galaxy-umsa.grid.cesnet.cz]
+        instance: [usegalaxy.cz, galaxy-umsa.grid.cesnet.cz, repeatexplorer-elixir.cerit-sc.cz]
         python-version: [3.11]
     steps:
       - uses: actions/checkout@v4

.github/workflows/dispatch_lint.yml

@@ -11,6 +11,7 @@ on:
         - galaxy-qa1.galaxy.cloud.e-infra.cz
         - usegalaxy.cz
         - galaxy-umsa.grid.cesnet.cz
+        - repeatexplorer-elixir.cerit-sc.cz
 
 jobs:
   build:

.github/workflows/dispatch_update.yml

@@ -15,6 +15,7 @@ on:
         - galaxy-qa1.galaxy.cloud.e-infra.cz
         - usegalaxy.cz
         - galaxy-umsa.grid.cesnet.cz
+        - repeatexplorer-elixir.cerit-sc.cz
 
 permissions:
   contents: write

.github/workflows/fix.yml

@@ -35,6 +35,8 @@ jobs:
           make INSTANCE=usegalaxy.cz fix
           make INSTANCE=galaxy-umsa.grid.cesnet.cz lint
           make INSTANCE=galaxy-umsa.grid.cesnet.cz fix
+          make INSTANCE=repeatexplorer-elixir.cerit-sc.cz lint
+          make INSTANCE=repeatexplorer-elixir.cerit-sc.cz fix
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v7
         with:

.github/workflows/lint.yml

@@ -32,3 +32,4 @@ jobs:
           make INSTANCE=galaxy-qa1.galaxy.cloud.e-infra.cz lint
           make INSTANCE=usegalaxy.cz lint
           make INSTANCE=galaxy-umsa.grid.cesnet.cz lint
+          make INSTANCE=repeatexplorer-elixir.cerit-sc.cz lint

Makefile

@@ -25,6 +25,6 @@ update-all: ## Run the update script for all repos
 	find ./$(INSTANCE) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P $(NPROC) python scripts/update_tool.py
 
 install: ## Run the Ephemeris command to install all repos and revisions that are missing from a given INSTANCE
-	find ./$(INSTANCE) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 1 -I {} shed-tools install --toolsfile {} --galaxy $(INSTANCE) --api_key $(GALAXY_API_KEY) --skip_install_resolver_dependencies
+	find ./$(INSTANCE) -name '*.yml.lock' | grep '^\./[^/]*/' | xargs -n 1 -P 1 -I {} shed-tools install --toolsfile {} --galaxy $(INSTANCE) --api_key $(GALAXY_API_KEY) --skip_install_resolver_dependencies
 
 .PHONY: fix lint help update-owner update-all install

repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml

@@ -0,0 +1,4 @@
+tool_panel_section_label: Assembly annotation tools
+tools:
+- name: repeat_annotation_pipeline3
+  owner: petr-novak

repeatexplorer-elixir.cerit-sc.cz/assembly_annotation_tools.yml.lock

@@ -0,0 +1,11 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: repeat_annotation_pipeline3
+  owner: petr-novak
+  revisions:
+  - 5366d5ea04bc
+  - 755a4d643184
+  tool_panel_section_id: assembly_annotation_tools
+  tool_panel_section_label: Assembly annotation tools

repeatexplorer-elixir.cerit-sc.cz/bed.yml

@@ -0,0 +1,6 @@
+tool_panel_section_label: BED
+tools:
+- name: gffread
+  owner: devteam
+- name: bedtools
+  owner: iuc

repeatexplorer-elixir.cerit-sc.cz/bed.yml.lock

@@ -0,0 +1,17 @@
+install_repository_dependencies: false
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tools:
+- name: gffread
+  owner: devteam
+  revisions:
+  - 3e436657dcd0
+  tool_panel_section_id: bed
+  tool_panel_section_label: BED
+- name: bedtools
+  owner: iuc
+  revisions:
+  - 2892111d91f8
+  - a1a923cd89e8
+  tool_panel_section_id: bed
+  tool_panel_section_label: BED