From 2dd88557fd41793a2585fdeafa9d4e7e4e044a89 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Fri, 13 Oct 2023 16:16:43 +0100 Subject: [PATCH] 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 --- .github/workflows/conda-templated.yaml | 10 ++++++++-- .github/workflows/ens_update_env_container.yaml | 4 ++-- .github/workflows/github-actions-runner.yaml | 2 +- .github/workflows/irap-fedora-ci-runner.yaml | 2 +- .github/workflows/scxa-solrcloud.yaml | 2 +- galaxy-jupyter-single-cell/image_tag | 2 +- galaxy-jupyter-single-cell/pre_install_dockerfile | 2 +- github-actions-runner/Dockerfile | 3 ++- 8 files changed, 17 insertions(+), 10 deletions(-) diff --git a/.github/workflows/conda-templated.yaml b/.github/workflows/conda-templated.yaml index 20e4a8c..6692e6b 100644 --- a/.github/workflows/conda-templated.yaml +++ b/.github/workflows/conda-templated.yaml @@ -8,6 +8,7 @@ on: paths: - "*/templated-conda-env.yaml" - "*/image_tag" + - "*/pre_install_dockerfile" - "*/post_install_dockerfile" - "miniconda_template/*" - ".github/workflows/miniconda_template.yaml" @@ -15,7 +16,7 @@ on: 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 index dc0ec50..ccd485a 100644 --- 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 index f7a91a3..81bbf6e 100644 --- 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 index 79bfc3b..b7e54d6 100644 --- 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 index a53450d..083914f 100644 --- 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 index c301692..ded22f9 100644 --- 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 index 59eb082..9bb7f3c 100644 --- 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 index 6a3661c..fc0d85e 100644 --- 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 && \