feat: migrate metatlas_shifter image to ghcr.io

biorack · Oct 10, 2023 · ee30837 · ee30837
1 parent 7f52320
commit ee30837
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Showing 4 changed files with 10 additions and 11 deletions.
diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
@@ -13,11 +13,12 @@ jobs:
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
-    - name: Login to DockerHub
+    - name: Login to GHCR
       uses: docker/login-action@v3
       with:
-        username: wjhjgi
-        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        registry: ghcr.io
+        username: ${{ github.repository_owner }}
+        password: ${{ secrets.GITHUB_TOKEN }}
     - name: generate version_info file
       run: python ./docker/most_recent_commits.py > docker/.version_info
     - name: generate time based tag
@@ -32,13 +33,11 @@ jobs:
         context: ./docker
         file: ./docker/Dockerfile.shifter
         platforms: linux/amd64
-        cache-from: type=registry,ref=wjhjgi/metatlas_shifter:latest
+        cache-from: type=registry,ref=ghcr.io/biorack/metatlas/metatlas_shifter:latest
         cache-to: type=inline
         tags: |
-          wjhjgi/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
-          wjhjgi/metatlas_shifter:latest
-          doejgi/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
-          doejgi/metatlas_shifter:latest
+          ghcr.io/biorack/metatlas/metatlas_shifter:${{ steps.timestamp.outputs.date_time }}
+          ghcr.io/biorack/metatlas/metatlas_shifter:latest
         push: true
   build_push_metatlas_analysis_image:
     name: Build/push analysis docker image

diff --git a/docker/rollback_shifter.sh b/docker/rollback_shifter.sh
@@ -9,7 +9,7 @@
 set -euf -o pipefail
 
 SHORT="metatlas_shifter"
-LONG="doejgi/$SHORT"
+LONG="ghcr.io/biorack/metatlas/$SHORT"
 TAG=""
 
 while [[ "$#" -gt 0 ]]; do

diff --git a/docker/shifter.kernel.json b/docker/shifter.kernel.json
@@ -1,4 +1,4 @@
 {"argv": ["shifter", "--module=none", "--clearenv", "--entrypoint",
-    "--image=doejgi/metatlas_shifter:latest",
+    "--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest",
     "/usr/local/bin/python", "-m", "ipykernel_launcher", "-f", "{connection_file}"],
     "display_name": "Metatlas Targeted", "language": "python", "metadata": {"debugger": true}}
diff --git a/papermill/submit_slurm_job.sh b/papermill/submit_slurm_job.sh
@@ -75,7 +75,7 @@ validate_extra_parameters() {
 }
 
 is_valid_yaml() {
-  echo "$1" | shifter --module=none --clearenv --image=doejgi/metatlas_shifter:latest \
+  echo "$1" | shifter --module=none --clearenv --image=ghcr.io/biorack/metatlas/metatlas_shifter:latest \
 	  /src/metatlas/scripts/yaml_validation.py
 }