genbank/rebuild #878
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |