Updates to docker

.github/workflows/docker-pangolin.yml

@@ -9,38 +9,40 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.2.2
 
       - name: Docker meta
         id: docker_meta
-        uses: crazy-max/ghaction-docker-meta@v1
+        uses: docker/[email protected]
         with:
           images: ghcr.io/bimberlabinternal/devops
-          tag-sha: true
-          tag-semver: |
-            {{version}}
-            {{major}}.{{minor}}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=sha
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3.2.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3.7.1
 
       - name: Login to GitHub Container Registry
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3.3.0
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.PAT }}
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6.10.0
         with:
           file: ./containers/pangolin/Dockerfile
           context: ./containers/pangolin
+          build-args: |
+            "GH_PAT=${{ secrets.PAT }}"
           pull: true
           push: true
           tags: ghcr.io/bimberlabinternal/pangolin:latest

.github/workflows/docker-paragraph.yml

@@ -8,11 +8,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
 
       - name: Docker meta
         id: docker_meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@v5.6.1
         with:
           images: ghcr.io/bimberlabinternal/paragraph
           tags: |
@@ -21,26 +21,22 @@ jobs:
             type=sha
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3.0.0
+        uses: docker/setup-qemu-action@v3.2.0
 
       - name: Set up Docker Buildx
-        uses: docker/[email protected]
-        with:
-          # Use the previous version of buildx to force docker to save a V1 image,
-          # since Exacloud's outdated docker version cannot handle V2/OCI:
-          version: v0.9.1
+        uses: docker/[email protected]
 
       - name: Login to GitHub Container Registry
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v3.1.0
+        uses: docker/login-action@v3.3.0
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.PAT }}
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5.3.0
+        uses: docker/build-push-action@v6.10.0
         with:
           file: ./containers/paragraph/Dockerfile
           context: ./containers/paragraph

servers/exacloud/config/pipelineConfig.xml

@@ -28,7 +28,7 @@
 						<entry key="JAVA_HOME" value="/home/exacloud/gscratch/prime-seq/java/current"/>
 						<entry key="JAVA_HOME_8" value="/home/exacloud/gscratch/prime-seq/java/java8"/>
 						<entry key="JAVA_HOME_7" value="/home/exacloud/gscratch/prime-seq/java/jdk1.7.0_55"/>
-						<entry key="DOCKER_EXE" value="/usr/local/bin/docker"/>
+						<entry key="DOCKER_EXE" value="/usr/bin/docker"/>
 						<entry key="SEQUENCEANALYSIS_MAX_THREADS" value="8"/>
 						<entry key="SEQUENCEANALYSIS_MAX_RAM" value="24"/>
 						<entry key="SEQUENCEANALYSIS_JAVA_OPTS" value="-Xss2m"/>