Add glycosylation annotation to B/Yam results #78
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| on: | |
| push: | |
| branches: | |
| - master | |
| - staging | |
| - release | |
| pull_request: | |
| repository_dispatch: | |
| types: build-and-deploy | |
| workflow_dispatch: | |
| workflow_call: | |
| concurrency: | |
| group: cli-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number || github.ref || github.run_id }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -euxo pipefail {0} | |
| env: | |
| GITHUB_REPOSITORY_URL: ${{ github.server_url }}/${{ github.repository }} | |
| VERBOSE: 1 | |
| jobs: | |
| build-and-deploy-datasets: | |
| runs-on: ubuntu-22.04 | |
| environment: | |
| name: ${{ github.ref }} | |
| env: | |
| VERBOSE: 0 | |
| PYTHONUNBUFFERED: 1 | |
| DATA_AWS_S3_BUCKET: ${{ secrets.DATA_AWS_S3_BUCKET }} | |
| DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID: ${{ secrets.DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| steps: | |
| - name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: "Authenticate git" | |
| run: | | |
| export GITHUB_TOKEN="${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }}" | |
| export BOT_GIT_USER_EMAIL="${{ secrets.BOT_GIT_USER_EMAIL }}" | |
| export BOT_GIT_USER_NAME="${{ secrets.BOT_GIT_USER_NAME }}" | |
| : ${GITHUB_TOKEN?"The env var GITHUB_TOKEN is required"} | |
| : ${BOT_GIT_USER_EMAIL?"The env var BOT_GIT_USER_EMAIL is required"} | |
| : ${BOT_GIT_USER_NAME?"The env var BOT_GIT_USER_NAME is required"} | |
| git config --global user.email "${BOT_GIT_USER_EMAIL}" | |
| git config --global user.name "${BOT_GIT_USER_NAME}" | |
| gh auth setup-git >/dev/null | |
| - name: "Extract branch name" | |
| run: | | |
| echo "current_branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT | |
| id: branch-name | |
| - name: "Checkout branch" | |
| run: | | |
| git fetch --all | |
| git switch ${{ steps.branch-name.outputs.current_branch }} | |
| - name: "Install system dependencies" | |
| run: | | |
| sudo apt-get install brotli pigz parallel python3 rename --yes -qq >/dev/null | |
| - name: "Install Python dependencies" | |
| run: | | |
| pip3 install -r requirements.txt | |
| - name: "Install awscli" | |
| run: | | |
| pushd /tmp >/dev/null | |
| curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" | |
| unzip -oqq awscliv2.zip | |
| sudo ./aws/install --update | |
| popd >/dev/null | |
| aws --version | |
| - name: "Rebuild, commit and push datasets" | |
| if: github.ref != 'refs/heads/release' | |
| run: | | |
| ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --push --repo="${GITHUB_REPOSITORY}" | |
| - name: "Rebuild, commit, push and make a release" | |
| if: github.ref == 'refs/heads/release' | |
| run: | | |
| ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --release --repo="${GITHUB_REPOSITORY}" | |
| - name: "Deploy dataset server" | |
| if: ${{ endsWith(github.ref, '/master') || endsWith(github.ref, '/staging') || endsWith(github.ref, '/release') }} | |
| run: | | |
| ./scripts/upload 'data_output/' | |
| - name: "Upload build artifacts: dataset server" | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: server | |
| path: ./data_output/* | |
| - name: "Upload build artifacts: zip archives" | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: zips | |
| path: ./data_temp/* |