Mac bioconda #1743
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| 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 |