Bioconda #9
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| name: Bioconda | |
| on: | |
| 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 | |
| run: | | |
| source /Users/runner/miniconda3/bin/activate | |
| echo CONDA_PREFIX = $CONDA_PREFIX | |
| bash ./test_stxtyper.sh path | |