GEO beds auto upload #8
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| name: GEO beds auto upload | |
| on: | |
| schedule: | |
| # run every day at 18:00 | |
| - cron: '0 18 * * *' | |
| workflow_dispatch: | |
| inputs: null | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: [ "3.12" ] | |
| os: [ ubuntu-latest ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install uv | |
| uv pip install torch==2.3.1+cpu -f https://download.pytorch.org/whl/torch_stable.html --system | |
| uv pip install git+https://github.com/databio/bedboss.git@dev#egg=bedboss --system | |
| - name: Get current date and date 2 days ago | |
| id: dates | |
| run: | | |
| echo "current_date=$(date +'%Y/%m/%d')" >> $GITHUB_ENV | |
| echo "date_2_days_ago=$(date -d '3 days ago' +'%Y/%m/%d')" >> $GITHUB_ENV | |
| - name: Print dates | |
| run: | | |
| echo "Hello, ${{ github.actor }}" | |
| echo "currect date: ${{ env.current_date }}" | |
| echo "date 2 days ago: ${{ env.date_2_days_ago }}" | |
| - name: Upload Project | |
| run: bedboss geo upload-all --outfolder /tmp/out --start-date ${{ env.date_2_days_ago }} --end-date ${{ env.current_date }} --no-use-skipper --lite --bedbase-config config.yaml --no-use-skipper --no-preload | |
| env: | |
| POSTGRES_HOST: ${{ secrets.POSTGRES_HOST }} | |
| POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }} | |
| POSTGRES_USER: ${{ secrets.POSTGRES_USER }} | |
| QDRANT_HOST: ${{ secrets.QDRANT_HOST }} | |
| QDRANT_API_KEY: ${{ secrets.QDRANT_API_KEY }} | |
| AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} |