rebuild-gisaid.yml

name: Rebuild GISAID phylogenetic datasets

on:
  # This workflow can be triggered from repository_dispatch events,
  # for instance, after the appropriate preprocessing actions have completed
  repository_dispatch:
    types:
      - rebuild
      - gisaid/rebuild
  # Manually triggered using GitHub's UI
  workflow_dispatch:
    inputs:
      trial_name:
        description: "Short name for this trial build, for prefixing the uploaded data and results files. WARNING: without this we will overwrite files in s3://nextstrain-ncov-private and the trees on nextstrain.org/ncov/gisaid..."
        required: false
      image:
        description: 'Specific container image to use for build (will override the default of "nextstrain build")'
        required: false

env:
  TRIAL_NAME: ${{ github.event.inputs.trial_name }}
  NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

jobs:
  gisaid:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2

    - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
      with:
        python-version: "3.9"

    - name: Launch build
      run: |
        set -x

        declare -a config
        config+=(build_date=\'$(date +'%Y-%m-%d')\')
        if [[ "$TRIAL_NAME" ]]; then
          config+=(
            S3_DST_BUCKET=nextstrain-ncov-private/trial/"$TRIAL_NAME"
            deploy_url=s3://nextstrain-staging/
            auspice_json_prefix=ncov_gisaid_trial_"$TRIAL_NAME"
          )
        else
          config+=(slack_token=$SLACK_TOKEN)
        fi

        nextstrain build \
          --aws-batch \
          --detach \
          --cpus 72 \
          --memory 140GiB \
          . \
            deploy \
            upload \
            --config "${config[@]}" \
            --profile nextstrain_profiles/nextstrain-gisaid \
            --set-threads tree=8 \
        |& tee build-launch.log
      env:
        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}

    - name: Build info
      run: |
        if [[ "$TRIAL_NAME" ]]; then
          echo "--> Trial name is: $TRIAL_NAME"
          echo
          echo "--> When completed, the following will be available:"
          echo "build files: s3://nextstrain-ncov-private/trial/$TRIAL_NAME/"
          echo "nextstrain URLs: https://nextstrain.org/staging/ncov/gisaid/trial/$TRIAL_NAME/REGION_NAME/TIME_SPAN"
          echo "e.g. https://nextstrain.org/staging/ncov/gisaid/trial/$TRIAL_NAME/global/all-time"
        else
          echo "--> GISAID phylogenetic analysis rebuilding on AWS"
          echo
          echo "--> When completed, the following will be updated:"
          echo "build files: s3://nextstrain-ncov-private/REGION_NAME/"
          echo "nextstrain URLs: https://nextstrain.org/ncov/gisaid/REGION_NAME/TIME_SPAN"
          echo "e.g. https://nextstrain.org/ncov/gisaid/global/all-time"
        fi
        echo
        echo "--> You can attach to this AWS job via:"
        tail -n1 build-launch.log
        echo
        JOBID=$( tail -n1 build-launch.log | sed -E 's/.+attach ([-a-f0-9]+).+/\1/' )
        echo "--> View this job in the AWS console via"
        echo "    https://console.aws.amazon.com/batch/home?region=us-east-1#jobs/detail/${JOBID}"
        echo