rebuild #259
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name: Rebuild hmpxv1-big | |
on: | |
repository_dispatch: | |
types: | |
- rebuild | |
- rebuild_hmpxv1-big | |
workflow_dispatch: | |
inputs: | |
trial_name: | |
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}" | |
required: false | |
image: | |
description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
required: false | |
jobs: | |
set_config_overrides: | |
runs-on: ubuntu-latest | |
steps: | |
- id: config | |
name: Set config overrides | |
env: | |
TRIAL_NAME: ${{ inputs.trial_name }} | |
run: | | |
config="" | |
if [[ "$TRIAL_NAME" ]]; then | |
config+="--config" | |
config+=" deploy_url='s3://nextstrain-staging/'" | |
config+=" auspice_prefix='"$TRIAL_NAME"'" | |
fi | |
echo "config=$config" >> "$GITHUB_OUTPUT" | |
outputs: | |
config_overrides: ${{ steps.config.outputs.config }} | |
rebuild_hmpxv1_big: | |
needs: [set_config_overrides] | |
permissions: | |
id-token: write | |
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
secrets: inherit | |
with: | |
runtime: aws-batch | |
env: | | |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }} | |
GITHUB_RUN_ID: ${{ github.run_id }} | |
SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }} | |
BUILD_DIR: phylogenetic | |
BUILD_NAME: hmpxv1_big | |
run: | | |
nextstrain build \ | |
--detach \ | |
--no-download \ | |
--cpus 8 \ | |
--memory 68gib \ | |
--env GITHUB_RUN_ID \ | |
--env SLACK_TOKEN \ | |
--env SLACK_CHANNELS \ | |
. \ | |
notify_on_deploy \ | |
--configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \ | |
$CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile |