conda-build-perl-convert-pheno #46
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| name: conda-build-perl-convert-pheno | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| # os: ["ubuntu-latest", "macos-latest"] | |
| os: ["ubuntu-latest"] | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: true | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| #mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 23.1.0-1 | |
| channels: conda-forge,bioconda | |
| activate-environment: build-env | |
| channel-priority: true | |
| use-only-tar-bz2: false # might break caching | |
| auto-update-conda: true | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache Conda env | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ | |
| steps.get-date.outputs.today }}-${{ | |
| hashFiles('conda_recipe/bioconda_utils-requirements.txt') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if conda_recipe/environment.yaml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Update environment | |
| run: | | |
| # conda install -n base conda-libmamba-solver | |
| # conda config --set solver libmamba | |
| # conda env update -n build-env -f conda_recipe/environment.yaml | |
| conda env update -n build-env -f conda_recipe/bioconda_utils-requirements.txt | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - shell: bash -el {0} | |
| run: | | |
| # conda config --set unsatisfiable_hints True | |
| # conda info | |
| # conda list | |
| # conda config --show-sources | |
| # conda config --show | |
| conda config --set always_yes yes | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| conda config --set unsatisfiable_hints True | |
| mamba info | |
| mamba list | |
| conda config --show-sources | |
| conda config --show | |
| printenv | sort | |
| - name: Run conda build | |
| shell: bash -el {0} | |
| run: | | |
| # conda mambabuild conda_recipe | |
| # conda build conda_recipe | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate build-env | |
| docker pull quay.io/dpryan79/mulled_container:latest | |
| export OSTYPE="linux-gnu" | |
| export CI="true" | |
| bioconda-utils build conda_recipe conda_recipe/config.yml \ | |
| --docker --mulled-test \ | |
| docker rmi quay.io/dpryan79/mulled_container:latest | |
| displayName: Test | |
| - name: Archive CPAN logs | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpan_log_${{ matrix.os }} | |
| path: /tmp/.cpanm/work/*/build.log |