Add MacOS to conda test #3
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| name: Bioconda | ||
| on: | ||
| push: | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: '30 10 * * *' # | ||
| repository_dispatch: | ||
| types: [linux-bioconda-test, install-test] | ||
| jobs: | ||
| x86_linux: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: When was this run | ||
| run: date | ||
| - name: configure conda | ||
| run: | | ||
| . $CONDA/bin/activate | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| - name: install StxTyper | ||
| run: | | ||
| . $CONDA/bin/activate | ||
| conda install --update-deps -c conda-forge -c bioconda --strict-channel-priority -y ncbi-stxtyper | ||
| stxtyper --version | ||
| - name: download tests | ||
| run: | | ||
| BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master | ||
| curl --silent --location -O ${BASE_URL}/test_stxtyper.sh | ||
| - name: run tests | ||
| run: | | ||
| source /usr/share/miniconda/bin/activate | ||
| echo CONDA_PREFIX = $CONDA_PREFIX | ||
| bash ./test_stxtyper.sh path | ||
| x86_mac: | ||
| runs-on: macos-latest | ||
| steps: | ||
| - name: Install conda b/c built-in conda was 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 $CONDA | ||
| conda update conda | ||
| - name: Install StxTyper | ||
| run: | | ||
| source /Users/runner/miniconda3/bin/activate | ||
| conda install --update-deps -c bioconda -c conda-forge -y ncbi-stxtyper | ||
| - name: Download tests | ||
| run: | | ||
| BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master | ||
| curl --silent --location -O ${BASE_URL}/test_stxtyper.sh | ||
| - name: Run tests | ||
| source /usr/share/miniconda/bin/activate | ||
| echo CONDA_PREFIX = $CONDA_PREFIX | ||
| bash ./test_stxtyper.sh path | ||
