major changes in the containers push

Author: ypriverol

.github/workflows/quantms-containers.yml

@@ -48,6 +48,14 @@ jobs:
         registry: ghcr.io
         username: ${{ github.actor }}
         password: ${{ secrets.GHCR_TOKEN }}
+    
+    - name: Install GitHub CLI
+      run: |
+        curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
+        echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null
+        sudo apt update
+        sudo apt install gh
+        gh auth login --with-token <<< "${{ secrets.GHCR_TOKEN }}"
 
     - name: Extract metadata for Docker
       id: meta
@@ -73,6 +81,8 @@ jobs:
         cache-from: type=gha
         cache-to: type=gha,mode=max
         provenance: false
+        
+    # Note: DiaNN containers remain private as per license requirements
 
     - name: Set up Singularity
       if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
@@ -106,6 +116,8 @@ jobs:
         # Push with version tag
         singularity push diann-2.1.0.sif oras://ghcr.io/bigbio/diann-sif:2.1.0
         
+        # Note: DiaNN containers remain private as per license requirements
+        
         # If this is a release event, also tag as latest
         if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
           singularity push diann-2.1.0.sif oras://ghcr.io/bigbio/diann-sif:latest
@@ -130,7 +142,8 @@ jobs:
       packages: write
 
     env:
-      OPENMS_VERSION: "2025.04.14"  # Manually defined version for OpenMS
+      # This version should be manually updated for each release
+      OPENMS_VERSION: "2025.04.12"  # Format: YYYY.MM.DD
 
     steps:
       - name: Checkout repository
@@ -145,6 +158,14 @@ jobs:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GHCR_TOKEN }}
+      
+      - name: Install GitHub CLI
+        run: |
+          curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
+          echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null
+          sudo apt update
+          sudo apt install gh
+          gh auth login --with-token <<< "${{ secrets.GHCR_TOKEN }}"
 
       - name: Pull OpenMS Docker container
         id: pull_docker
@@ -172,6 +193,13 @@ jobs:
             docker push $TARGET_CONTAINER
           }
           
+          # Make the package public
+          echo "Making package public"
+          gh api --method PATCH /orgs/bigbio/packages/container/openms-tools-thirdparty/visibility \
+            -f visibility="public" \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28"
+          
           # If this is a release push or a GitHub release event, also tag as latest
           if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
             LATEST_IMAGE="ghcr.io/bigbio/openms-tools-thirdparty:latest"
@@ -225,6 +253,13 @@ jobs:
             singularity push openms-tools-thirdparty.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:${{ env.OPENMS_VERSION }}
           }
           
+          # Make the SIF package public
+          echo "Making SIF package public"
+          gh api --method PATCH /orgs/bigbio/packages/container/openms-tools-thirdparty-sif/visibility \
+            -f visibility="public" \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28"
+          
           # If this is a release push or a GitHub release event, also tag as latest
           if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
             echo "Pushing OpenMS SIF as latest"

README.md

@@ -21,27 +21,30 @@ These containerized versions offer:
 
 ### DIA-NN Containers
 
-quantms team do not distribute the DIANN containers for versions superior to 1.8.0. The user has to build the container locally using the following command:
+**Important**: Due to licensing restrictions, DiaNN containers are not publicly distributed. Users must build these containers locally:
 
 ```bash
+# Build Docker container
+cd diann-2.1.0/
 docker build -t diann:2.1.0 .
-```
-
-To build the singularity container, the user has to run the following command:
 
-```bash
+# Build Singularity container from Docker
 singularity build diann-2.1.0.sif docker-daemon://diann:2.1.0
 ```
 
 ### OpenMS Containers
 
+OpenMS containers are publicly available and can be pulled directly:
+
 | Container Type | Version | URL |
 |----------------|---------|-----|
 | Docker | date-tagged | `ghcr.io/bigbio/openms-tools-thirdparty:YYYY.MM.DD` |
 | Docker | latest | `ghcr.io/bigbio/openms-tools-thirdparty:latest` |
 | Singularity | date-tagged | `oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:YYYY.MM.DD` |
 | Singularity | latest | `oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest` |
 
+The date tag (YYYY.MM.DD) is manually set for each release to ensure version stability.
+
 ## ⚠️ Important License Information
 
 Please note the following license restrictions:
@@ -169,6 +172,37 @@ Common issues and solutions:
    - Increase Docker memory allocation in Docker Desktop settings
    - Use `--memory` flag to specify container memory limit
 
+3. **OpenMS Singularity Pull Issues**
+   
+   If you encounter an error when pulling OpenMS Singularity images:
+   ```
+   FATAL: While pulling image from oci registry: error fetching image to cache: failed to get checksum for oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:YYYY.MM.DD: GET https://ghcr.io/v2/bigbio/openms-tools-thirdparty-sif/manifests/YYYY.MM.DD: DENIED: requested access to the resource is denied
+   ```
+   
+   Try the following:
+   
+   - Verify you're using the correct date tag format (YYYY.MM.DD)
+   - Check the workflow logs to confirm the exact version tag that was published
+   - If using Nextflow, try increasing the pull timeout:
+     ```
+     nextflow run bigbio/quantms -r dev -profile test_lfq,singularity -with-singularity --singularity.pullTimeout '2h'
+     ```
+   - If the issue persists, please open an issue on the GitHub repository
+
+4. **DiaNN Container Issues**
+   
+   Remember that DiaNN containers must be built locally due to licensing restrictions:
+   
+   - Follow the build instructions in the "DiaNN Containers" section
+   - For quantms pipeline, specify your local DiaNN container path in a custom config file:
+     ```yaml
+     process {
+         withLabel: diann {
+             container = '/path-to-your-singularity-file/diann-2.1.0.sif'
+         }
+     }
+     ```
+
 ## Maintainers
 
 - Yasset Perez-Riverol ([@ypriverol](https://github.com/ypriverol)) - [ypriverol@gmail.com](mailto:ypriverol@gmail.com)