new gh action to synchronize bioconductor to biotools

Author: hmenager

bioconductor-to-biotools/action.yml

@@ -0,0 +1,32 @@
+name: 'Update Bioconductor bio.tools files'
+description: 'Bioconductor to bio.tools synchronization'
+inputs:
+  repo-user:  # id of input
+    description: 'User that commits modifications'
+    required: true
+  repo-token:
+    description: 'GitHub token to commit modifications'
+    required: true
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Install bc2bt
+      run:
+        pip install -r ${{ github.action_path }}/requirements.txt
+        pip install ${{ github.action_path }}
+      shell: bash
+    - name: Synchronize Bioconductor to bio.tools
+      run: |
+        bc2bt sync imports/bioconductor data --work-dir /tmp/bc2bt_work
+      shell: bash
+    - name: reformat json to a predictable format with jq and sponge
+      run: |
+        sudo apt-get update -y
+        sudo apt-get install moreutils
+        FILES='data/*/*.biotools.json'
+        for f in $FILES; do jq --indent 4 'walk( if type == "array" then sort else . end )'  $f | sponge $f; echo "processed $f file!"; done
+      shell: bash