diff --git a/.github/workflows/docker_all-modules.yml b/.github/workflows/docker_all-modules.yml index b383b5624..1e82c4a4a 100644 --- a/.github/workflows/docker_all-modules.yml +++ b/.github/workflows/docker_all-modules.yml @@ -43,6 +43,7 @@ jobs: - cell-type-nonETP-ALL-03 - cell-type-ETP-ALL-03 - cell-type-consensus + - seurat-conversion uses: ./.github/workflows/build-push-docker-module.yml if: github.repository_owner == 'AlexsLemonade' with: diff --git a/.github/workflows/run_all-modules.yml b/.github/workflows/run_all-modules.yml index 1a007b096..7886ec6f7 100644 --- a/.github/workflows/run_all-modules.yml +++ b/.github/workflows/run_all-modules.yml @@ -43,6 +43,9 @@ jobs: cell-type-consensus: uses: ./.github/workflows/run_cell-type-consensus.yml + seurat-conversion: + uses: ./.github/workflows/run_seurat-conversion.yml + ## Add additional modules above this comment, and to the needs list below check-jobs: if: ${{ always() }} @@ -56,6 +59,7 @@ jobs: - cell-type-ETP-ALL-03 - cell-type-nonETP-ALL-03 - cell-type-consensus + - seurat-conversion runs-on: ubuntu-latest steps: - name: Checkout template file diff --git a/.github/workflows/run_seurat-conversion.yml b/.github/workflows/run_seurat-conversion.yml index 6348f40c1..4c27dc0ed 100644 --- a/.github/workflows/run_seurat-conversion.yml +++ b/.github/workflows/run_seurat-conversion.yml @@ -33,27 +33,20 @@ jobs: run-module: if: github.repository_owner == 'AlexsLemonade' runs-on: ubuntu-latest + container: public.ecr.aws/openscpca/seurat-conversion:latest + defaults: + run: + shell: bash -el {0} steps: - name: Checkout repo uses: actions/checkout@v4 - - name: Set up R - uses: r-lib/actions/setup-r@v2 - with: - r-version: 4.4.0 - use-public-rspm: true - - - name: Install additional dependencies + - name: Install aws-cli run: | - sudo apt-get install -y \ - libhdf5-dev \ - libglpk40 - - - name: Set up renv - uses: r-lib/actions/setup-renv@v2 - with: - working-directory: ${{ env.MODULE_PATH }} + curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" + unzip awscliv2.zip + ./aws/install - name: Download test data env: