daylily-ephemeral-cluster 5.1.23

Infrastructure-as-code for ephemeral AWS ParallelCluster environments for bioinformatics

Daylily Ephemeral Cluster

DayEC is the operator control plane for short-lived AWS ParallelCluster environments that run Daylily analysis workloads on FSx for Lustre. The current data plane is DRA-first: the cluster starts with reference data mounted at /fsx/references, run folders are attached only when needed under /fsx/run_dir_mounts/<mount_id>, workflow outputs stay under /fsx/analysis_results/<executing_entity>/<analysis_id>, and completed analysis directories are exported through a temporary direct DRA to a chosen S3 analysis bucket.

The cluster is ephemeral. S3 buckets are durable. Verify the export receipt before deleting the cluster.

Supported Operator Contract

Use the checkout environment and the CLI, not historical helper-script paths:

1. source ./activate
2. dyec preflight
3. dyec create
4. dyec headnode connect
5. dyec samples stage for sample-manifest inputs, or dyec mounts create for run-folder inputs
6. dyec workflow launch
7. dyec export --source-path /fsx/analysis_results/<executing_entity>/<analysis_id> --destination-s3-uri s3://bucket/prefix/<executing_entity>/<analysis_id>/
8. inspect fsx_export.yaml
9. dyec delete --dry-run
10. dyec delete

daylily-ec and dyec are the same entrypoint. The shorter dyec form is used in examples.

One Copy-Pasteable Lifecycle

source ./activate

export AWS_PROFILE=daylily-service-lsmc
export REGION=us-west-2
export REGION_AZ=us-west-2d
export CLUSTER_NAME=day-demo-$(date +%Y%m%d%H%M%S)
export DAY_EX_CFG="$HOME/.config/daylily/daylily_ephemeral_cluster.yaml"
export REF_S3_URI=s3://lsmc-dayoa-references-usw2
export CONTROL_DATA_S3_URI=s3://lsmc-dayoa-control-data-usw2
export STAGE_S3_URI=s3://lsmc-ssf-sequencing-data/staged_external_data
export ANALYSIS_BUCKET=s3://lsmc-dayoa-analysis-results-us-west-2
export EXECUTING_ENTITY="${USER:-ubuntu}"
export ANALYSIS_ID=dayoa
export ANALYSIS_SAMPLES=etc/analysis_samples_template.tsv
export STAGE_CFG_DIR="$PWD/tmp-stage-config/$CLUSTER_NAME"
export EXPORT_DIR="$PWD/tmp-export/$ANALYSIS_ID"
export EXPORT_S3_URI="$ANALYSIS_BUCKET/analysis_results/$EXECUTING_ENTITY/$ANALYSIS_ID/"

dyec preflight \
  --profile "$AWS_PROFILE" \
  --region-az "$REGION_AZ" \
  --config "$DAY_EX_CFG"

dyec create \
  --profile "$AWS_PROFILE" \
  --region-az "$REGION_AZ" \
  --config "$DAY_EX_CFG"

dyec headnode connect \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME"

dyec samples stage "$ANALYSIS_SAMPLES" \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --reference-s3-uri "$REF_S3_URI" \
  --control-data-s3-uri "$CONTROL_DATA_S3_URI" \
  --stage-s3-uri "$STAGE_S3_URI" \
  --config-dir "$STAGE_CFG_DIR"

dyec workflow launch \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME" \
  --stage-dir "/fsx/staging/staged_external_sequencing_data/remote_stage_<timestamp>" \
  --analysis-id "$ANALYSIS_ID" \
  --executing-entity "$EXECUTING_ENTITY" \
  --git-tag 2.0.29 \
  --export-destination-s3-uri "$EXPORT_S3_URI" \
  --export-trigger on-success

# For run-folder work, attach only the S3 prefix you need.
dyec --json mounts create "s3://sequencer-run-bucket/runs/RUN123/" \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME" \
  --platform ILMN \
  --read-only \
  --wait

dyec --json mounts verify \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME" \
  --mount-id RUN123

dyec workflow launch \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME" \
  --run-context-file ./runs.tsv \
  --analysis-id "<run-analysis-id>" \
  --executing-entity "$EXECUTING_ENTITY" \
  --git-tag 2.0.29 \
  --dy-command "bin/day_run produce_illumina_run_qc --config run_context_file=config/runs.tsv -p -j 5 -k"

dyec export \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME" \
  --source-path "/fsx/analysis_results/$EXECUTING_ENTITY/$ANALYSIS_ID" \
  --destination-s3-uri "$EXPORT_S3_URI" \
  --output-dir "$EXPORT_DIR"

cat "$EXPORT_DIR/fsx_export.yaml"

dyec delete --dry-run \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME"

dyec delete \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster "$CLUSTER_NAME"

Architecture At A Glance

flowchart LR
  Ref["S3 reference bucket /data/"] -->|reference-data DRA| Data["/fsx/references"]
  Run["S3 run prefix"] -->|ephemeral run DRA| Mount["/fsx/run_dir_mounts/<mount_id>"]
  Data --> Workflow["DayOA workflow"]
  Mount --> Workflow
  Workflow --> Results["/fsx/analysis_results/..."]
  Results --> Export["temporary direct export DRA on /analysis_results/<executing_entity>/<analysis_id>/"]
  Export -->|EXPORT_TO_REPOSITORY| Analysis["S3 analysis bucket prefix /<executing_entity>/<analysis_id>/"]

Key rules:

• /fsx/references is the reference-data DRA created with the cluster.
• /fsx/run_dir_mounts/<mount_id> is for read-oriented run inputs and is not an export source.
• /fsx/analysis_results/... is where workflow checkouts and outputs live.
• dyec export creates a temporary DRA on the exact completed analysis directory, runs EXPORT_TO_REPOSITORY, and detaches it with DeleteDataInFileSystem=false.
• fsx_export.yaml is the v3 export receipt to keep before teardown.

Pipeline Catalog

config/daylily_pipeline_command_catalog.yaml is the source of truth for repositories and blessed launch profiles. The packaged copy under daylily_ec/resources/payload/config/ must match it.

The current DayOA pin is 2.0.29 for the repository default and every DayOA command. Catalog v2 separates:

• sample_analysis: uses analysis_samples.tsv, stages inputs, and writes samples.tsv / units.tsv.
• run_analysis: uses runs.tsv, requires a run DRA, and launches run-folder workflows such as Illumina run QC and BCL Convert.

Each test_data_profile declares how source data is expected to appear on FSx:

• source_mount_mode: default_mounted means the source prefix is already exposed by the cluster's default /fsx/references or /fsx/control_data DRAs.
• source_mount_mode: run_dra_required means the exact run prefix comes from runs.tsv SOURCE_S3_URI; DYEC must verify or create the matching /fsx/run_dir_mounts/<MOUNT_ID>/ DRA before launch.
• source_mount_mode: none means the command does not consume external sample or run source data.

The catalog records the primary source_s3_uri_template, source_fsx_prefix, and, for run-analysis profiles, the required SOURCE_S3_URI and MOUNT_ID run-context columns. Historical or alternate validation roots stay in profile notes and test_data_locations.

For BCL Convert run-analysis launches, DYEC patches the active DayOA profile for direct mounted input, zero barcode mismatches, merge_lane_fastqs: false, and shared_thread_odirect_output: false; the launcher then hard-requires a DayOA checkout that exposes native lane-split BCL rules and lane-level downstream report consumption.

Dewey Registration And QEO MultiQC Loading

Dewey registration is supported as a DYEC export concern. DayOA emits local evidence manifests only; it does not receive Dewey or QEO configuration. DYEC maps DayOA evidence relative paths through fsx_export.yaml, registers the selected artifacts with Dewey, and lets Dewey emit QEO outbox events. QEO loading is then requested through Dewey, not through DYEC.

The live contract is intentionally strict:

• config/daylily_pipeline_command_catalog.yaml must contain an explicit artifact_registration policy for the command.
• The exported DayOA tree must contain the evidence manifest selected by that policy, or an explicit s3-inventory registration must be requested.
• Every registered file artifact must have a SHA-256 digest. Do not substitute an S3 ETag for SHA-256.
• config/samples.tsv and config/units.tsv are registered when present. Their metadata and tags include sample names plus unique unit-table values such as EXPERIMENTID, RUNID, LANEID, BARCODEID, LIBPREP, SEQ_VENDOR, and SEQ_PLATFORM.
• MultiQC HTML and MultiQC data-dir artifacts carry the same sample and unit context in Dewey artifact metadata, plus report-kind tags such as report_kind:final, report_kind:run_qc, or report_kind:bclconvert.

Register During Export

Use this path for a completed analysis directory that is still on FSx and needs to be exported to S3 and registered with Dewey in one operation:

source ./activate

export AWS_PROFILE=daylily-service-lsmc
export REGION=us-west-2
export DEWEY_URL=https://dewey.example
export DEWEY_TOKEN_ENV=DEWEY_TOKEN
export DEWEY_TOKEN='<dewey bearer token>'
export EXECUTING_ENTITY=ubuntu
export ANALYSIS_ID=ccv20260530r50_illumina_hg002_kitchensink_multiqc
export EXPORT_S3_URI="s3://bucket/derived/validation/dyec-test/$EXECUTING_ENTITY/$ANALYSIS_ID/"
export EXPORT_DIR="$PWD/tmp-export/$ANALYSIS_ID"

dyec export \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --cluster-name "<cluster-name>" \
  --source-path "/fsx/analysis_results/$EXECUTING_ENTITY/$ANALYSIS_ID" \
  --destination-s3-uri "$EXPORT_S3_URI" \
  --output-dir "$EXPORT_DIR" \
  --artifact-registration-command-id illumina_hg002_kitchensink_multiqc \
  --dewey-url "$DEWEY_URL" \
  --dewey-token-env "$DEWEY_TOKEN_ENV"

Successful registration writes:

• $EXPORT_DIR/fsx_export.yaml
• $EXPORT_DIR/dewey_registration_receipt.json

Check the receipt before requesting QEO loading:

jq '.fsx_export.dewey_registration_status,
    .fsx_export.dewey_selected_artifact_count,
    .fsx_export.dewey_multiqc_artifact_set_count' \
  "$EXPORT_DIR/fsx_export.yaml"

jq '.analysis_response.artifact_set_euid,
    .multiqc_responses[].artifact_set_euid' \
  "$EXPORT_DIR/dewey_registration_receipt.json"

Register An Existing Export

Use exports register-dewey only when the analysis directory has already been exported to S3 and you do not want to create a new DRA or export task:

dyec exports register-dewey \
  --profile "$AWS_PROFILE" \
  --region "$REGION" \
  --source-path "/fsx/analysis_results/$EXECUTING_ENTITY/$ANALYSIS_ID" \
  --destination-s3-uri "$EXPORT_S3_URI" \
  --output-dir "$EXPORT_DIR" \
  --artifact-registration-command-id illumina_hg002_kitchensink_multiqc \
  --manifest-source dayoa-manifest \
  --dewey-url "$DEWEY_URL" \
  --dewey-token-env "$DEWEY_TOKEN_ENV"

Use --manifest-source s3-inventory only for exported prefixes where every selected S3 object has SHA-256 metadata or an S3 SHA-256 checksum. Older FSx DRA exports commonly do not have that metadata, so this mode should fail before any Dewey POST rather than registering weakly identified objects.

Run-analysis commands with multiple MultiQC reports use their own command ID. For Illumina run QC plus BCL Convert, use:

--artifact-registration-command-id illumina_run_qc_bclconvert

That policy registers both:

• results/runs/**/run_qc/illumina/multiqc_report.html
• results/runs/**/bclconvert/multiqc_report.html

and their corresponding multiqc_report_data/ files.

Request QEO Loading Through Dewey

DYEC does not call QEO directly and does not carry a QEO URL or QEO token. Successful Dewey registration creates Dewey outbox events:

• lsmc.dewey.artifact_set.registered.v1
• lsmc.dewey.multiqc_artifact_set.registered.v1

Dewey now has filtered QEO dispatch support. In the Dewey checkout for the target deployment:

source ./activate <deploy-name>

dewey qeo status

dewey qeo dispatch \
  --artifact-set-euid "<multiqc-artifact-set-euid-from-dewey_registration_receipt.json>" \
  --limit 10

If the operator has the outbox event ID instead of the artifact-set EUID, use:

dewey qeo dispatch --event-id "<dewey-outbox-event-id>" --limit 10

The dispatch command requires Dewey QEO config to be explicit and valid:

• qeo.ingest_url must be an absolute https:// URL for QEO's Dewey event ingest endpoint.
• qeo.api_token must be present.
• qeo.consumer_group must be present.

A good QEO loading request should include:

• the DYEC fsx_export.yaml path,
• the DYEC dewey_registration_receipt.json path,
• the analysis artifact-set EUID,
• every MultiQC artifact-set EUID to dispatch,
• whether to dispatch by --artifact-set-euid or exact --event-id,
• the expected QEO evidence: ingest ledger rows, parsed metric counts, and dead-letter state.

If Dewey registration did not complete, there is nothing for QEO to load. Fix registration first by providing SHA-256-complete DayOA evidence manifests, re-exporting with SHA-256 metadata, or explicitly changing the Dewey checksum contract.

What This Repo Ships

• source ./activate: creates or repairs the DAY-EC environment and installs the checkout editable
• dyec / daylily-ec: preflight, create, headnode, sample, workflow, mount, export, delete, state, repository, pricing, and AWS validation commands
• DRA-backed ParallelCluster templates under config/day_cluster/
• packaged resources under daylily_ec/resources/payload/
• day-clone for headnode repository checkouts
• tests that guard the catalog, packaged resources, SSM behavior, DRA mounts, export receipts, and environment contract

Read This Next

• docs/dra_fsx_strategy.md: current DRA-enabled FSx strategy and diagrams
• docs/ultra_rapid_start.md: shortest current run path
• docs/quickest_start.md: guided walkthrough with checks
• docs/operations.md: day-2 operations
• docs/cli_reference.md: command reference
• docs/pipeline_manager_launches.md: Snakemake 7, Snakemake 8, Nextflow, and Cromwell launch contracts
• docs/aws_setup.md: AWS prerequisites
• docs/monitoring_and_troubleshooting.md: failure triage
• docs/testing_and_debugging.md: local and AWS-backed validation
• docs/DAY_EC_ENVIRONMENT.md: environment contract
• docs/pip_install.md: pip install path
• docs/archive/README.md: historical material only