Update panaroo to 1.5.0 (#46944) #1
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| name: Upload | |
| on: | |
| push: | |
| branches: | |
| - master | |
| jobs: | |
| build-linux: | |
| name: Linux Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 13 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and upload | |
| env: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -ex | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| docker pull quay.io/dpryan79/mulled_container:latest | |
| # bioconda-utils handle-merged-pr recipes config.yml \ | |
| # --repo bioconda/bioconda-recipes \ | |
| # --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \ | |
| # --quay-upload-target biocontainers \ | |
| # --fallback build | |
| bioconda-utils build recipes config.yml \ | |
| --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers | |
| docker rmi quay.io/dpryan79/mulled_container:latest | |
| build-osx: | |
| name: OSX Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: macOS-latest | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and Test | |
| env: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| # The SDK isn't actually cached, so reinstall it | |
| run_conda_forge_build_setup | |
| # bioconda-utils handle-merged-pr recipes config.yml \ | |
| # --repo bioconda/bioconda-recipes \ | |
| # --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \ | |
| # --fallback build | |
| bioconda-utils build recipes config.yml \ | |
| --anaconda-upload --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} |