mac_conda.yml

name: Mac bioconda
on:
    workflow_dispatch:
    schedule:
        - cron: '15 9 * * *' # 9:15am everyday
    repository_dispatch:
        types: [mac-bioconda-test, install-test]
jobs:
  build:
    runs-on: macos-latest
    steps:
    - name: Install conda because built-in conda is borked
      run: |
          curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
          bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/runner/miniconda3
    - name: Configure conda
      run: |
          source /Users/runner/miniconda3/bin/activate
          conda init
          # THIS DOESN"T WORK! Just install miniconda myself
          # . $CONDA/bin/activate
          conda config --add channels defaults
          conda config --add channels bioconda
          conda config --add channels conda-forge
          # permissions are messed up on the mac runner
          # Is this faster than installing miniconda myself?
          # sudo chown -R 501:20 $CONDA
          conda update conda
    - name: Install AMRFinderPlus
      run: |
          source /Users/runner/miniconda3/bin/activate
          conda install --update-deps -c bioconda -c conda-forge -y ncbi-amrfinderplus
    - name: Download AMRFinderPlus database
      run: |
          source /Users/runner/miniconda3/bin/activate
          /Users/runner/miniconda3/bin/amrfinder -u
    - name: Software and DB version
      run: |
          source /Users/runner/miniconda3/bin/activate
          amrfinder --database_version
    - name: Download tests
      run: |
          BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
          curl --silent -L \
             -O ${BASE_URL}/test_dna.fa \
             -O ${BASE_URL}/test_prot.fa \
             -O ${BASE_URL}/test_prot.gff \
             -O ${BASE_URL}/test_both.expected \
             -O ${BASE_URL}/test_dna.expected \
             -O ${BASE_URL}/test_dna_mut_all.expected \
             -O ${BASE_URL}/test_prot.expected \
             -O ${BASE_URL}/test_amrfinder.sh
    - name: Run tests
      run: |
          source /Users/runner/miniconda3/bin/activate
          echo CONDA_PREFIX = $CONDA_PREFIX
          bash ./test_amrfinder.sh path