barcode update #295
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| name: barcode update | |
| on: | |
| schedule: | |
| - cron: '0 0 * * *' | |
| jobs: | |
| testsuite: | |
| runs-on: macos-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@main | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: bioconda,conda-forge | |
| channel-priority: true | |
| python-version: 3.7 | |
| activate-environment: test | |
| - name: Install | |
| shell: bash -l {0} | |
| run: | | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda install --yes --file ci/conda_requirements.txt | |
| pip install -e . --no-deps | |
| - name: update | |
| shell: bash -l {0} | |
| env: | |
| TREELINK: ${{ secrets.TREELINK }} | |
| ZIPNAME: ${{ secrets.ZIPNAME }} | |
| run: | | |
| conda activate test | |
| wget "${TREELINK}" | |
| freyja barcode-build --pb "${ZIPNAME}" --outdir freyja/data/ | |
| - name: commit if output is different | |
| run: | | |
| echo "running git diff, committing if different" | |
| if [[($(git status freyja/data/usher_barcodes.csv --porcelain | wc -c) -ne 0)]]; then | |
| echo "changes were made, updating barcodes" | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| echo $(date +"%m_%d_%Y-%H-%M")> freyja/data/last_barcode_update.txt | |
| git add freyja/data/last_barcode_update.txt | |
| git add freyja/data/lineages.yml | |
| git add freyja/data/usher_barcodes.csv | |
| git add freyja/data/curated_lineages.json | |
| git commit -m "updating barcodes and metadata" | |
| git push origin main | |
| else | |
| echo "no changes were made, doing nothing." | |
| fi; | |