genbank/rebuild #877
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| name: Rebuild open (GenBank) 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 | |
| - open/rebuild | |
| - genbank/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-data/files/ncov/open/ and the trees on nextstrain.org/ncov/open/..." | |
| 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: ${{ github.event.inputs.image }} | |
| jobs: | |
| open: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| - name: Launch build | |
| run: | | |
| set -x | |
| declare -a config | |
| config+=(build_date=\'$(date +'%Y-%m-%d')\') | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=( | |
| S3_DST_BUCKET=nextstrain-staging/files/ncov/open/trial/"$TRIAL_NAME" | |
| deploy_url=s3://nextstrain-staging/ | |
| auspice_json_prefix=ncov_open_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-open \ | |
| --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: $TRIAL_NAME" | |
| echo | |
| echo "--> When completed, the following will be available:" | |
| echo "build files: s3://nextstrain-staging/files/ncov/open/trial/$TRIAL_NAME/" | |
| echo "nextstrain URLs: https://nextstrain.org/staging/ncov/open/trial/$TRIAL_NAME/REGION_NAME/TIME_SPAN" | |
| echo "e.g. https://nextstrain.org/staging/ncov/open/trial/$TRIAL_NAME/global/all-time" | |
| else | |
| echo "--> Open (GenBank) phylogenetic analysis rebuilding on AWS" | |
| echo | |
| echo "--> When completed, the following will be updated:" | |
| echo "build files: s3://nextstrain-data/files/ncov/open/REGION_NAME/" | |
| echo "nextstrain URLs: https://nextstrain.org/ncov/open/REGION_NAME/TIME_SPAN" | |
| echo "e.g. https://nextstrain.org/ncov/open/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 |