Merge pull request #1 from martenson/test_lint

adjustments to makefile, test linting workflow on PR

Author: martenson

.github/workflows/lint.yml

@@ -1,8 +1,6 @@
 name: Tool linting
 
 on:
-  # push:
-  #   branches: [ main ]
   pull_request:
     branches: [ main ]
   workflow_dispatch:
@@ -31,4 +29,6 @@ jobs:
           python -m pip install --upgrade pip
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Perform linting
-        run: make pr_check
+        run: |
+          make INSTANCE=galaxy-qa1.galaxy.cloud.e-infra.cz lint
+          make INSTANCE=usegalaxy.cz lint

Makefile

@@ -22,10 +22,7 @@ update-trusted:  ## Run the update script for a subset of repos defined by the O
 update-all: ## Run the update script for all repos
 	find ./$(INSTANCE) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update_tool.py
 
-# shed-tools install --install_resolver_dependencies --toolsfile $< --galaxy $(GALAXY_SERVER) --api_key $(GALAXY_API_KEY) 2>&1 | tee -a report.log
+install: ## Run the Ephemeris command to install all repos and revisions that are missing from a given INSTANCE
+	find ./$(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
 
-# shed-tools install --toolsfile $< --galaxy $(GALAXY_SERVER) --api_key $(GALAXY_API_KEY)
-
-# shed-tools install -g "$URL" -t tool_list.yaml.lock --log_level ERROR --log-file "$LOG"
-
-.PHONY: fix lint help update-trusted update-all
+.PHONY: fix lint help update-trusted update-all install

galaxy-qa1.galaxy.cloud.e-infra.cz/nanopore.yml.lock

@@ -66,42 +66,49 @@ tools:
   owner: iuc
   revisions:
   - 543cbeef3949
+  - a2899db6bd6e
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_squiggle
   owner: iuc
   revisions:
+  - 26e6c9362b7b
   - ce8af9373061
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_occupancy
   owner: iuc
   revisions:
+  - 0433aad600e9
   - 336791b5665f
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_hist
   owner: iuc
   revisions:
   - 47936349f3e9
+  - d1805f9c4c82
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_yield_plot
   owner: iuc
   revisions:
   - 64a83664b814
+  - c5c5a3e84989
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_qualpos
   owner: iuc
   revisions:
   - 2e22ebec211a
+  - 626b6c2be5c2
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: poretools_events
   owner: iuc
   revisions:
   - 1d835c691480
+  - daf8518d243a
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: medaka_variant