Move to ubuntu-latest and single cell Jupyter (#140)

* Move to ubuntu latest * Comment to trigger docker build * Master seems frozen for 6 months now * Comment change to trigger build * Trigger action * Change tag * Try freeing up space * Remove extra ls
ebi-gene-expression-group · Oct 13, 2023 · 2dd8855 · 2dd8855
1 parent cbb2ec4
commit 2dd8855
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Showing 8 changed files with 17 additions and 10 deletions.
diff --git a/.github/workflows/conda-templated.yaml b/.github/workflows/conda-templated.yaml
@@ -8,14 +8,15 @@ on:
     paths:
       - "*/templated-conda-env.yaml"
       - "*/image_tag"
+      - "*/pre_install_dockerfile"
       - "*/post_install_dockerfile"
       - "miniconda_template/*"
       - ".github/workflows/miniconda_template.yaml"
 
 jobs:
   getchanges:
     name: Get changed repos
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
@@ -45,7 +46,7 @@ jobs:
 
   test:
     name: Build image and optionally deploy
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     needs: getchanges
     strategy:
       matrix:
@@ -74,6 +75,11 @@ jobs:
     - name: Assemble Dockerfile
       run: miniconda_template/create_dockerfile.sh ${{ matrix.changed }}
 
+    - name: Free up some space for building large images
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
     - name: Build image
       id: build-image
       uses: redhat-actions/buildah-build@v2

diff --git a/.github/workflows/ens_update_env_container.yaml b/.github/workflows/ens_update_env_container.yaml
@@ -11,7 +11,7 @@ on:
 jobs:
   test:
     name: Build image
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       IMAGE_NAME: ensembl-update-env
 
@@ -34,7 +34,7 @@ jobs:
           
   deploy:
     name: Build and deploy image to quay.io/ebigxa
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       IMAGE_NAME: ensembl-update-env
 

diff --git a/.github/workflows/github-actions-runner.yaml b/.github/workflows/github-actions-runner.yaml
@@ -8,7 +8,7 @@ on:
 jobs:
   build:
     name: Build and push image
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       IMAGE_NAME: github-actions-runner
 

diff --git a/.github/workflows/irap-fedora-ci-runner.yaml b/.github/workflows/irap-fedora-ci-runner.yaml
@@ -13,7 +13,7 @@ on:
 jobs:          
   deploy:
     name: Build and deploy image to quay.io/ebigxa
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.github/workflows/scxa-solrcloud.yaml b/.github/workflows/scxa-solrcloud.yaml
@@ -8,7 +8,7 @@ on:
 jobs:
   build:
     name: Build and push image
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       IMAGE_NAME: scxa-solrcloud
 

diff --git a/galaxy-jupyter-single-cell/image_tag b/galaxy-jupyter-single-cell/image_tag
@@ -1 +1 @@
-pseq-galaxy-jupyter-single-cell:0.1
+pseq-galaxy-jupyter-single-cell:0.2
diff --git a/galaxy-jupyter-single-cell/pre_install_dockerfile b/galaxy-jupyter-single-cell/pre_install_dockerfile
@@ -1,5 +1,5 @@
-# uses the same image as the original interactive environment in Galaxy
 FROM quay.io/bgruening/docker-jupyter-notebook:2021-03-05
+# uses the same image as the original interactive environment in Galaxy
 
 # install micromamba
 RUN "${SHELL}" <(curl -L micro.mamba.pm/install.sh)

diff --git a/github-actions-runner/Dockerfile b/github-actions-runner/Dockerfile
@@ -1,4 +1,5 @@
-FROM quay.io/evryfs/github-actions-runner:master
+FROM quay.io/evryfs/github-actions-runner:latest
+# based on
 
 USER root
 RUN sudo apt-key adv --refresh-keys --keyserver keyserver.ubuntu.com && \