singularity_container-install.yml

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@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
        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* ]] ; then
            echo "::set-output name=keepgoing::true"
          else
            echo "::set-output name=keepgoing::false"
          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 "##[set-output name=location;]$(echo "  - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")"
        id: extract_location

      - name: Build Container
        run: |
          ls container
          cd container
          wget https://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.17.1/ncbi-igblast-1.17.1-x64-linux.tar.gz
          wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz
          tar -xzvf ncbi-igblast-1.17.1-x64-linux.tar.gz
          tar -xzvf ncbi-blast-2.12.0+-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