genbank/rebuild #905
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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 |