getting rid of CI warnings #804
Workflow file for this run
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| name: Test Singularity Build | |
| on: | |
| # push: | |
| # branches: | |
| # - master | |
| # Do the builds on all pull requests (to test them) | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| changes: | |
| name: Checking changed files | |
| runs-on: ubuntu-latest | |
| outputs: | |
| changed_file: ${{ steps.files.outputs.added_modified }} | |
| keepgoing: ${{ steps.checkfiles.outputs.keepgoing }} | |
| steps: | |
| - id: files | |
| uses: jitterbit/get-changed-files@v1 | |
| with: | |
| format: 'json' | |
| - id: checkfiles | |
| run: | | |
| if [[ ${{ steps.files.outputs.added_modified }} == *.yml* || ${{ steps.files.outputs.added_modified }} == *.py* || ${{ steps.files.outputs.added_modified }} == *test* || ${{ steps.files.outputs.added_modified }} == *requirements* || ${{ steps.files.outputs.added_modified }} == *database* ]] ; then | |
| echo "keepgoing=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "keepgoing=false" >> $GITHUB_OUTPUT | |
| fi | |
| container: | |
| needs: | |
| - changes | |
| if: needs.changes.outputs.keepgoing == 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Go 1.13 | |
| uses: actions/setup-go@v1 | |
| with: | |
| go-version: 1.13 | |
| id: go | |
| - name: Install Dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config | |
| - name: Install Singularity | |
| env: | |
| SINGULARITY_VERSION: 3.8.1 | |
| GOPATH: /tmp/go | |
| run: | | |
| mkdir -p $GOPATH | |
| sudo mkdir -p /usr/local/var/singularity/mnt && \ | |
| mkdir -p $GOPATH/src/github.com/sylabs && \ | |
| cd $GOPATH/src/github.com/sylabs && \ | |
| wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \ | |
| tar xzv && \ | |
| cd singularity-ce-${SINGULARITY_VERSION} && \ | |
| ./mconfig -p /usr/local && \ | |
| make -C builddir && \ | |
| sudo make -C builddir install | |
| - name: Check out code for the container build | |
| uses: actions/checkout@v2 | |
| - name: Extract repository location | |
| shell: bash | |
| run: | | |
| echo "location=$(echo " - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT | |
| id: extract_location | |
| - name: Build Container | |
| run: | | |
| ls container | |
| cd container | |
| wget https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.19.0/ncbi-igblast-1.19.0-x64-linux.tar.gz | |
| wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-x64-linux.tar.gz | |
| tar -xzvf ncbi-igblast-1.19.0-x64-linux.tar.gz | |
| tar -xzvf ncbi-blast-2.13.0+-x64-linux.tar.gz | |
| echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml | |
| sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def | |
| - name: Test Container | |
| run: | | |
| cd container | |
| sudo singularity test --writable-tmpfs sc-dandelion.sif | |
| singularity run -B $PWD sc-dandelion.sif dandelion-preprocess --help |