Switch Singularity to Apptainer in GitHub Actions CI workflow

genomic-medicine-sweden · Jan 17, 2025 · 0540cc4 · 0540cc4
1 parent 9766efc
commit 0540cc4
Showing 1 changed file with 3 additions and 7 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -50,15 +50,11 @@ jobs:
         run: |
           cd ${GITHUB_WORKSPACE} && make check-and-reinit-git-submodules
 
-      - name: Install Singularity
-        # For running (locally) with ACT, we use a docker image with Singularity already installed
+      - name: Install Apptainer
+        # For running (locally) with ACT, we use a docker image with Singularity/Apptainer already installed
         if: "${{ ! github.event.act }}"
         run: |
-          wget https://github.com/apptainer/singularity/releases/download/v3.8.7/singularity-container_3.8.7_amd64.deb && sudo dpkg -i singularity-container_3.8.7_amd64.deb
-
-      - name: Create symlink to apptainer command
-        run: |
-          sudo ln -s /usr/bin/singularity /usr/bin/apptainer
+          wget https://github.com/apptainer/apptainer/releases/download/v1.3.6/apptainer_1.3.6_amd64.deb && sudo dpkg -i apptainer_1.3.6_amd64.deb
 
       - name: Install containers
         run: