getting rid of CI warnings #808
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v35 | |
| with: | |
| files: | | |
| **/*.{yml,py} | |
| container/database | |
| container/tests | |
| container/*.{yml,py} | |
| tests | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| echo ${{ steps.changed-files.outputs.any_changed }} | |
| - name: Get if changed files need to continue | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "keepgoing=true" >> $GITHUB_OUTPUT | |
| 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 |