Galaxy

.github/workflows/galaxy_autoupdate.yml

@@ -0,0 +1,73 @@
+name: Galaxy wrapper autoupdate
+
+# Polls Bioconda for a newer beegees release and opens a PR bumping the
+# Galaxy wrapper to it. The PR is merged by hand so the wrapper can be
+# checked against any new pipeline options; galaxy_tag.yml then tags it.
+on:
+  schedule:
+    - cron: "0 6 * * *"   # daily, 06:00 UTC
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  autoupdate:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Compare Bioconda and wrapper versions
+        id: versions
+        run: |
+          latest=$(curl -sf https://api.anaconda.org/package/bioconda/beegees | jq -r .latest_version)
+          if [ -z "$latest" ] || [ "$latest" = "null" ]; then
+            echo "::error::Could not read latest beegees version from Bioconda"
+            exit 1
+          fi
+          current=$(sed -n 's:.*<token name="@TOOL_VERSION@">\(.*\)</token>.*:\1:p' beegees/galaxy/macros.xml)
+          echo "Bioconda: $latest, wrapper: $current"
+          newest=$(printf '%s\n%s\n' "$current" "$latest" | sort -V | tail -n 1)
+          if [ "$latest" != "$current" ] && [ "$newest" = "$latest" ]; then
+            echo "update=true" >> "$GITHUB_OUTPUT"
+          fi
+          echo "latest=$latest" >> "$GITHUB_OUTPUT"
+          echo "current=$current" >> "$GITHUB_OUTPUT"
+
+      - name: Bump macros.xml
+        if: steps.versions.outputs.update == 'true'
+        env:
+          LATEST: ${{ steps.versions.outputs.latest }}
+        run: |
+          sed -i \
+            -e "s:<token name=\"@TOOL_VERSION@\">[^<]*</token>:<token name=\"@TOOL_VERSION@\">${LATEST}</token>:" \
+            -e "s:<token name=\"@VERSION_SUFFIX@\">[^<]*</token>:<token name=\"@VERSION_SUFFIX@\">0</token>:" \
+            beegees/galaxy/macros.xml
+          git diff
+
+      # A PAT is needed so the PR push triggers the lint/test workflows;
+      # pushes made with GITHUB_TOKEN do not start other workflows.
+      - name: Open pull request
+        if: steps.versions.outputs.update == 'true'
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.GALAXY_AUTOUPDATE_TOKEN }}
+          base: main
+          branch: galaxy-autoupdate
+          delete-branch: true
+          add-paths: beegees/galaxy/macros.xml
+          commit-message: "galaxy: bump beegees to ${{ steps.versions.outputs.latest }}"
+          title: "galaxy: bump beegees ${{ steps.versions.outputs.current }} -> ${{ steps.versions.outputs.latest }}"
+          body: |
+            Bioconda has published beegees ${{ steps.versions.outputs.latest }}.
+
+            This PR sets `@TOOL_VERSION@` to ${{ steps.versions.outputs.latest }} and resets
+            `@VERSION_SUFFIX@` to 0. Merging it tags
+            `galaxy-${{ steps.versions.outputs.latest }}+galaxy0`, which uploads to the Tool Shed.
+
+            Before merging:
+            - [ ] Lint and planemo tests pass
+            - [ ] New or changed pipeline options are reflected in `beegees.xml`
+            - [ ] Test data still matches the new outputs

.github/workflows/galaxy_tag.yml

@@ -0,0 +1,36 @@
+name: Tag Galaxy wrapper release
+
+# When macros.xml changes on main (an autoupdate PR or a manual
+# VERSION_SUFFIX bump), tag galaxy-<TOOL_VERSION>+galaxy<VERSION_SUFFIX>
+# if that tag doesn't exist yet. The tag triggers toolshed_deploy.yml.
+on:
+  push:
+    branches: [main]
+    paths:
+      - "beegees/galaxy/macros.xml"
+
+permissions:
+  contents: read
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+      # A PAT is needed so the tag push triggers toolshed_deploy.yml;
+      # pushes made with GITHUB_TOKEN do not start other workflows.
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GALAXY_AUTOUPDATE_TOKEN }}
+
+      - name: Create and push release tag
+        run: |
+          tool_version=$(sed -n 's:.*<token name="@TOOL_VERSION@">\(.*\)</token>.*:\1:p' beegees/galaxy/macros.xml)
+          suffix=$(sed -n 's:.*<token name="@VERSION_SUFFIX@">\(.*\)</token>.*:\1:p' beegees/galaxy/macros.xml)
+          tag="galaxy-${tool_version}+galaxy${suffix}"
+          if [ -n "$(git ls-remote --tags origin "refs/tags/$tag")" ]; then
+            echo "Tag $tag already exists, nothing to release"
+            exit 0
+          fi
+          git tag "$tag"
+          git push origin "$tag"
+          echo "Pushed $tag"

.github/workflows/toolshed_deploy.yml

@@ -0,0 +1,87 @@
+name: Deploy to Galaxy Tool Shed
+
+on:
+  push:
+    branches:
+      - "**"
+    # GitHub ignores path filters for tag pushes, so tags always run
+    paths:
+      - "beegees/galaxy/**"
+      - ".github/workflows/toolshed_deploy.yml"
+    tags:
+      # Galaxy wrapper releases only, e.g. galaxy-3.0.4+galaxy4.
+      # Package tags (v*) drive Bioconda and must not upload to the Tool Shed.
+      - "galaxy-*"
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install planemo
+        run: pip install planemo
+
+      - name: Lint tool XML
+        run: planemo lint beegees/galaxy/beegees.xml
+
+  test:
+    needs: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install planemo
+        run: pip install planemo
+
+      - name: Run tool tests
+        run: |
+          planemo test \
+            --galaxy_branch release_24.1 \
+            --conda_auto_install \
+            --conda_auto_init \
+            --test_data beegees/galaxy/test-data/ beegees/galaxy/beegees.xml 
+
+  shed_upload:
+    needs: test
+    if: startsWith(github.ref, 'refs/tags/galaxy-')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Check tag matches macros.xml version
+        run: |
+          tool_version=$(sed -n 's:.*<token name="@TOOL_VERSION@">\(.*\)</token>.*:\1:p' beegees/galaxy/macros.xml)
+          suffix=$(sed -n 's:.*<token name="@VERSION_SUFFIX@">\(.*\)</token>.*:\1:p' beegees/galaxy/macros.xml)
+          expected="galaxy-${tool_version}+galaxy${suffix}"
+          if [ "$GITHUB_REF_NAME" != "$expected" ]; then
+            echo "::error::Tag $GITHUB_REF_NAME does not match macros.xml ($expected)"
+            exit 1
+          fi
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install planemo
+        run: pip install planemo
+
+      - name: Upload to Tool Shed
+        env:
+          TOOLSHED_API_KEY: ${{ secrets.TOOLSHED_API_KEY }}
+        run: |
+          planemo shed_upload \
+            --shed_target toolshed \
+            --shed_key "$TOOLSHED_API_KEY" \
+            beegees/galaxy/

.gitignore

@@ -8,3 +8,6 @@ build/
 *.log
 .DS_Store
 .pytest_cache/
+
+# Galaxy instance-specific data table entries (only .loc.sample files are shipped)
+beegees/galaxy/tool-data/*.loc

beegees/galaxy/.shed.yml

@@ -0,0 +1,25 @@
+name: beegees
+owner: bge-barcoding # needs to be created on toolshed (could be the name of the maintainer, Dan?)
+description: BeeGees — DNA barcoding from genome skims
+long_description: |
+  BeeGees recovers DNA barcodes from low-coverage genome skim data.
+  It wraps fastp QC, gene-fetch reference retrieval, MitoGeneExtractor barcode
+  extraction, fasta_cleaner sequence cleaning, structural validation (HMM +
+  reading-frame checks), taxonomic validation (BLASTn), and MultiQC reporting
+  into a single Snakemake pipeline.
+homepage_url: https://github.com/bge-barcoding/BeeGees
+remote_repository_url: https://github.com/bge-barcoding/BeeGees
+categories:
+  - Sequence Analysis
+  - Metagenomics
+
+# Only these files are uploaded to the Tool Shed — the rest of the repo is excluded
+include:
+  - beegees.xml
+  - macros.xml
+  - build_samples_csv.py
+  - build_config_yaml.py
+  - tool_data_table_conf.xml.sample
+  - tool-data/blastdb.loc.sample
+  - tool-data/beegees_blast_taxonomy.loc.sample
+  - test-data/*