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AWS HealthOmics Tools

SDK and CLI Tools for working with the AWS HealthOmics Service.

Installation

AWS HealthOmics Tools is available through pypi. To install, type:

pip install aws-healthomics-tools

Install from source

Installing from source requires that your machine has the following prerequisites installed:

  • python3.10 or above
  • poetry package manager
  • make build tool
git clone https://github.com/awslabs/aws-healthomics-tools.git
cd ./aws-healthomics-tools
make install

SDK Tools

HealthOmics Transfer Manager

Basic Usage

The TransferManager class makes it easy to download files from a AWS HealthOmics reference or read set. By default the files are saved to the current directory, or you can specify a custom location with the directory parameter.

import boto3
from omics.common.omics_file_types import ReadSetFileName, ReferenceFileName, ReadSetFileType
from omics.transfer.manager import TransferManager
from omics.transfer.config import TransferConfig

REFERENCE_STORE_ID = "<my-reference-store-id>"
SEQUENCE_STORE_ID = "<my-sequence-store-id>"

client = boto3.client("omics")
manager = TransferManager(client)

# Download all files for a reference.
manager.download_reference(REFERENCE_STORE_ID, "<my-reference-id>")

# Download all files for a read set to a custom directory.
manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>", "my-sequence-data")

Download specific files

Specific files can be downloaded via the download_reference_file and download_read_set_file methods. The client_fileobj parameter can be either the name of a local file to create for storing the data, or a TextIO or BinaryIO object that supports write methods.

# Download a specific reference file.
manager.download_reference_file(
    REFERENCE_STORE_ID,
    "<my-reference-id>",
    ReferenceFileName.INDEX
)

# Download a specific read set file with a custom filename.
manager.download_read_set_file(
    SEQUENCE_STORE_ID,
    "<my-read-set-id>",
    ReadSetFileName.INDEX,
    "my-sequence-data/read-set-index"
)

Upload specific files

Specific files can be uploaded via the upload_read_set method. The fileobjs parameter can be either the name of a local file, or a TextIO or BinaryIO object that supports read methods. For paired end reads, you can define fileobjs as a list of files.

# Upload a specific read set file.
read_set_id = manager.upload_read_set(
    "my-sequence-data/read-set-file.bam",
    SEQUENCE_STORE_ID,
    "BAM",
    "name",
    "subject-id",
    "sample-id",
    "<my-reference-arn>",
)

# Upload paired end read set files.
read_set_id = manager.upload_read_set(
    ["my-sequence-data/read-set-file_1.fastq.gz", "my-sequence-data/read-set-file_2.fastq.gz"],
    SEQUENCE_STORE_ID,
    "FASTQ",
    "name",
    "subject-id",
    "sample-id",
    "<my-reference-arn>",
)

Subscribe to events

Transfer events: on_queued, on_progress, and on_done can be observed by defining a subclass of OmicsTransferSubscriber and passing in an object which can receive events.

class ProgressReporter(OmicsTransferSubscriber):
    def on_queued(self, **kwargs):
        future: OmicsTransferFuture = kwargs["future"]
        print(f"Download queued: {future.meta.call_args.fileobj}")

    def on_done(self, **kwargs):
        print("Download complete")

manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>", subscribers=[ProgressReporter()])

Threads

Transfer operations use threads to implement concurrency. Thread use can be disabled by setting the use_threads attribute to False.

If thread use is disabled, transfer concurrency does not occur. Accordingly, the value of the max_request_concurrency attribute is ignored.

# Disable thread use/transfer concurrency
config = TransferConfig(use_threads=False)
manager = TransferManager(client, config)
manager.download_read_set(SEQUENCE_STORE_ID, "<my-read-set-id>")

HealthOmics URI Parser

The OmicsUriParser class makes it easy to parse AWS HealthOmics readset and reference URIs to extract fields relevant for calling AWS HealthOmics APIs.

Readset file URI:

Readset file URIs come in the following format:

omics://<AWS_ACCOUNT_ID>.storage.<AWS_REGION>.amazonaws.com/<SEQUENCE_STORE_ID>/readSet/<READSET_ID>/<SOURCE1/SOURCE2>

For example:

omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/readSet/5346184667/source1
omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/readSet/5346184667/source2

Reference file URI:

Reference file URIs come in the following format:

omics://<AWS_ACCOUNT_ID>.storage.<AWS_REGION>.amazonaws.com/<REFERENCE_STORE_ID>/reference/<REFERENCE_ID>/source

For example:

omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/reference/5346184667/source

To handle both HealthOmics URI types, you would use code like the following:

import boto3
from omics.uriparse.uri_parse import OmicsUriParser, OmicsUri

READSET_URI_STRING = "omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/readSet/5346184667/source1"
REFERENCE_URI_STRING = "omics://123412341234.storage.us-east-1.amazonaws.com/5432154321/reference/5346184667/source"

client = boto3.client("omics")

readset = OmicsUriParser(READSET_URI_STRING).parse()
reference = OmicsUriParser(REFERENCE_URI_STRING).parse()

# use the parsed fields from the URIs to call AWS HealthOmics APIs:

manager = TransferManager(client)

# Download all files for a reference.
manager.download_reference(reference.store_id, reference.resource_id)

# Download all files for a read set to a custom directory.
manager.download_read_set(readset.store_id, readset.resource_id, readset.file_name)

# Download a specific read set file with a custom filename.
manager.download_read_set_file(
    readset.store_id,
    readset.resource_id,
    readset.file_name,
    "my-sequence-data/read-set-index"
)

CLI Tools

CLI tools are modules in this package that can be invoked from the command line with:

python -m omics.cli.<TOOL-NAME>

HealthOmics Rerun

The rerun tool makes it easy to start a new run execution from a CloudWatch Logs manifest.

For an overview of what it does and available options run:

aws-healthomics-tools rerun -h

List runs from manifest

The following example lists all workflow run ids which were completed on July 1st (UTC time):

aws-healthomics-tools rerun -s 2023-07-01T00:00:00 -e 2023-07-02T00:00:00

this returns something like:

1234567 (2023-07-01T12:00:00.000)
2345678 (2023-07-01T13:00:00.000)

Rerun a previously-executed run

To rerun a previously-executed run, specify the run id you would like to rerun:

aws-healthomics-tools rerun 1234567

this returns something like:

StartRun request:
{
  "workflowId": "4974161",
  "workflowType": "READY2RUN",
  "roleArn": "arn:aws:iam::123412341234:role/MyRole",
  "parameters": {
    "inputFASTQ_2": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R2_001-5x.fastq.gz",
    "inputFASTQ_1": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.gz"
  },
  "outputUri": "s3://my-bucket/my-path"
}
StartRun response:
{
  "arn": "arn:aws:omics:us-west-2:123412341234:run/3456789",
  "id": "3456789",
  "status": "PENDING",
  "tags": {}
}

It is possible to override a request parameter from the original run. The following example tags the new run, which is particularly useful as tags are not propagated from the original run.

aws-healthomics-tools rerun 1234567 --tag=myKey=myValue

this returns something like:

StartRun request:
{
  "workflowId": "4974161",
  "workflowType": "READY2RUN",
  "roleArn": "arn:aws:iam::123412341234:role/MyRole",
  "parameters": {
    "inputFASTQ_2": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R2_001-5x.fastq.gz",
    "inputFASTQ_1": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.gz"
  },
  "outputUri": "s3://my-bucket/my-path",
  "tags": {
    "myKey": "myValue"
  }
}
StartRun response:
{
  "arn": "arn:aws:omics:us-west-2:123412341234:run/4567890",
  "id": "4567890",
  "status": "PENDING",
  "tags": {
    "myKey": "myValue"
  }
}

Before submitting a rerun request, it is possible to dry-run to view the new StartRun request:

aws-healthomics-tools rerun -d 1234567

this returns something like:

StartRun request:
{
  "workflowId": "4974161",
  "workflowType": "READY2RUN",
  "roleArn": "arn:aws:iam::123412341234:role/MyRole",
  "parameters": {
    "inputFASTQ_2": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R2_001-5x.fastq.gz",
    "inputFASTQ_1": "s3://omics-us-west-2/sample-inputs/4974161/HG002-NA24385-pFDA_S2_L002_R1_001-5x.fastq.gz"
  },
  "outputUri": "s3://my-bucket/my-path"
}

HealthOmics Run Analyzer

The run_analyzer tool retrieves a workflow run manifest from CloudWatchLogs and generates statistics for the run, including CPU and memory utilization for each workflow task.

For an overview of what it does and available options run:

aws-healthomics-tools run_analyzer -h

List completed runs

The following example lists all workflow runs completed in the past 5 days:

aws-healthomics-tools run_analyzer -t5d

this returns something like:

Workflow run IDs (<completionTime> <UUID>):
1234567 (2024-02-01T12:00:00 12345678-1234-5678-9abc-123456789012)
2345678 (2024-02-03T13:00:00 12345678-1234-5678-9abc-123456789012)

Analyze a specific workflow run

aws-healthomics-tools run_analyzer 1234567 -o run-1234567.csv
Providing a UUID

If a run ID is ambiguous, you can provide a UUID along with the run ID in the following way:

aws-healthomics-tools run_analyzer 1234567:2eca9876-ac33-98cd-0298-11cc59c05273 -o run-1234567.csv

this returns something like:

omics-run-analyzer: wrote run-1234567.csv
Output Columns

The CSV output by the command above includes the following columns:

  • uuid : Globally unique identifier to identify runs across accounts and regions
  • arn : Unique workflow run or task identifier
  • type : Resource type (run or task)
  • name : Workflow run or task name
  • startTime : Start timestamp for the workflow run or task (UTC time)
  • stopTime : Stop timestamp for the workflow run or task (UTC time)
  • runningSeconds : Approximate workflow run or task runtime (in seconds)
  • cpusRequested : The number of vCPU requested by the workflow task
  • gpusRequested : The number of GPUs requested by the workflow task
  • memoryRequestedGiB : Gibibytes of memory requested by the workflow task
  • omicsInstanceTypeReserved : Requested HealthOmics instance type for each task
  • omicsInstanceTypeMinimum : Minimum HealthOmics instance type that could run each task.
  • recommendedCpus: The number of CPUs recommended for this task (corresponding to the number of CPUs in the omicsInstanceTypeMinimum)
  • recommendedMemoryGiB: The amount of GiB of memory recommended for this task (corresponding to the number of CPUs in the omicsInstanceTypeMinimum)
  • estimatedUSD : Estimated HealthOmics charges (USD) for the workflow based on sizeReserved and runningSeconds
  • minimumUSD : Estimated HealthOmics charges (USD) for the workflow based on the recommended omicsInstanceTypeMinimum and runningSeconds
  • cpuUtilizationRatio : CPU utilization (cpusMaximum / cpusReserved) for workflow task(s)
  • memoryUtilizationRatio : Memory utilization (memoryMaximumGiB / memoryReservedGiB) for the workflow task(s)
  • storageUtilizationRatio : Storage utilization (storageMaximumGiB / storageReservedGiB) for the workflow run
  • cpusReserved : vCPUs reserved for workflow task(s)
  • cpusMaximum : Maximum vCPUs used during a single 1-minute interval
  • cpusAverage : Average vCPUs used by workflow task(s)
  • gpusReserved : GPUs reserved for workflow task(s)
  • memoryReservedGiB : Gibibytes of memory reserved for workflow task(s)
  • memoryMaximumGiB : Maximum gibibytes of memory used during a single 1-minute interval
  • memoryAverageGiB : Average gibibytes of memory used by workflow task(s)
  • storageReservedGiB : Gibibytes of storage reserved for the workflow run
  • storageMaximumGiB : Maximum gibibytes of storage used during a single 1-minute interval
  • storageAverageGiB : Average gibibytes of storage used by the workflow run

For rows that are a task type, the maximums, averages and reserved columns refer to the maximum, average or reserved amounts of the respective resource used by that task. These values can be used to guide the resources that should be requested for that task. For rows that are a run type the maximums, averages and reserved columns refer to the maximum, average or reserved amounts of the respective resource used concurrently by that run. These values can be used to determine if the accounts HealthOmics active CPUs/memory limits are being reached which might indicate the run is constrained by these limits.

Run Optimization and Estimated Cost Reduction

Based on the metrics observed and calculated for a run, the application will recommend the smallest instance type that could be used for each task in the run. The type is reported in the omicsInstanceTypeMinimum column. To obtain this type for a task you can set the task CPU and memory requested for the task to the values of recommendedCpus and recommendedMemoryGiB in you workflow definition. Based on this change each task would be estimated to reduce the cost of the run by estimatedUSD minus minimumUSD. The total potential cost reduction for the entire run can be estimated by subtracting the minimumUSD value from the estimatedUSD value in the row where the type is "run".

Add headroom to recommendations

Sometimes you will see variance in the amount of memory and CPU used in a run task, especially if you expect to run workflows with larger input files than were used in the analyzed run. For this reason you might want to allow add some headroom to the recommendations produced by the the run analyzer.

The -H or --headroom flag can be use to add an additional 0.0 to 1.0 times the max CPU or memory used by a task to the calculation used to determine the omicsInstanceTypeMinimum recommendation. For example if a task used a max of 3.6 GiB of memory and the headroom value is 0.5 then 6 GiB of memory - math.ceil(3.6 * (1 + 0.5)) - will be used to determine the minimum instance type that should be used.

If your analyzed run is already close to optimal then adding headroom might result in the recommended minimum instance being larger than the instance used in the run which will also cause the "minimumUSD" to be larger than the "estimatedUSD".

Use CloudWatch run metrics

HealthOmics publishes near real-time run metrics (aws.omics.*) to CloudWatch for runs whose service role allows cloudwatch:PutMetricData. Add --cloudwatch to include them in the analysis:

aws-healthomics-tools run_analyzer 1234567 --cloudwatch -o run-1234567.csv

The metrics are queried with PromQL in the run's region. This requires cloudwatch:GetMetricData and cloudwatch:ListMetrics, and CloudWatch bills PromQL API queries per million samples scanned (a typical run analysis scans very few samples). Run the analyzer in the account that started the run; metrics are not available in other accounts.

When any task has CloudWatch data, these columns are appended to the CSV (cells are blank where a metric is unavailable):

  • metricsSource : Which source determined the CPU and memory sizing basis: cloudwatch (both), mixed (one of them) or manifest (neither, e.g. no CloudWatch data, or the manifest memory peak was higher)
  • cwCpusMaximum, cwCpusP95, cwCpusAverage : vCPUs used (peak, 95th percentile, mean of 30-second samples)
  • cwCpuUtilizationRatio : cwCpusP95 / cpusReserved
  • cpuIdleFraction : Fraction of samples where the task used less than 25% of its vCPUs
  • cwMemoryMaximumGiB, cwMemoryP95GiB, cwMemoryAverageGiB : Memory used
  • cwMemoryUtilizationRatio : cwMemoryMaximumGiB / memoryReservedGiB
  • memoryPressure : True when peak memory reached 90% of the enforced limit (risk of out-of-memory failures)
  • scratchStorageMode, scratchMaximumGiB, scratchLimitGiB, scratchUtilizationRatio, scratchPressure : Task scratch storage use (the limit is only reported in LOCAL mode)
  • gpuUtilizationAverage, gpuUtilizationMaximum (%), gpuMemoryMaximumGiB, gpusIdle : GPU use; a GPU is idle if its utilization never exceeded 5%
  • recommendedGpus : GPUs that were actually used
  • cwStorageMaximumGiB : Peak run shared-filesystem use (run row)
  • fsReadGiB, fsWriteGiB, fsReadOps, fsWriteOps, netReceiveGiB, netTransmitGiB : Task I/O totals
  • fsThroughputMiBps, fsOpsPerSecond, netThroughputMiBps : Average I/O rates over the task runtime
  • ioBound : True when average CPU use was below 30% while filesystem or network throughput was at least 100 MiB/s or filesystem operations at least 1000/s; such tasks are unlikely to benefit from more CPUs

When CloudWatch data is available, CPU recommendations use the 95th-percentile vCPUs (a CPU-starved task only slows down). Memory recommendations use the larger of the CloudWatch and manifest peaks, because running out of memory fails the task and 30-second samples can miss short peaks. CloudWatch memory usage is often lower than the manifest value because the two are measured with a different scope; compare cwMemoryMaximumGiB with memoryMaximumGiB if you want to size more aggressively. Missing or zero CloudWatch values fall back to the manifest, per task and per metric. A GPU task whose GPUs all stayed idle is sized onto a CPU instance.

Batch mode (--batch) adds aggregated CloudWatch columns (for example maximumCwCpusP95, anyMemoryPressure, cloudwatchCount); tasks without CloudWatch data are excluded from these aggregates rather than counted as zero. With --plot, vCPU and memory usage-versus-reserved charts are drawn under the timeline.

Missing metrics never stop the analysis. Runs without metrics (runs that predate run metrics, run roles without cloudwatch:PutMetricData, runs with LogLevel OFF, runs older than the 15-month CloudWatch retention, or Regions without PromQL querying), missing permissions, and tasks that ran for less than about 30 seconds produce a notice on stderr, and the manifest values are used. --show --cloudwatch embeds the metrics in the JSON output (cloudwatchMetrics); re-analyzing that file with --file --cloudwatch reuses them without querying CloudWatch again, unless the earlier query was incomplete (failed queries, or a run that had only just finished), in which case it queries again. Without --cloudwatch, embedded metrics are ignored. The --plot charts are always queried from CloudWatch.

Produce a timeline plot for a run

The RunAnalyzer tool can produce an interative timeline plot of a workflow. The plots allow you to visualize how individual tasks ran over the course of the run.

aws-healthomics-tools run_analyzer -P plots/ 7113639

Example time line image showing stacked horizontal bars indicating the time taken by each task

Output workflow run manifest in JSON format

aws-healthomics-tools run_analyzer 1234567 -s -o run-1234567.json

this returns something like:

omics-run-analyzer: wrote run-1234567.json

Output optimized configuration

The --write-config option will write a new configuration file with the recommendedCpus and recommendedMemoryGiB as the resource requirements. This will take the maximum values if the task is run multiple times with different inputs.

aws-healthomics-tools run_analyzer 123456 --write-config=optimized.config

Aggregate scattered tasks and multiple runs (batch mode)

The --batch option can be used with a single run to aggregate all scattered tasks into one summarized task report. Non scattered tasks are also aggregated but will have a count of 1.

aws-healthomics-tools run_analyzer 1234567 --batch

The option may also be used with multiple runs to aggregate all tasks including scattered tasks.

aws-healthomics-tools run_analyzer 1234567 2345678 3456789 --batch

These statics are reported in CSV format:

  • "type": The type of row (currently always task),
  • "name": The base name of the task with any scatter suffix removed
  • "count": The number of times the named task has been observed in the runs
  • "meanRunningSeconds": The average runtime in seconds for the named tasks
  • "maximumRunningSeconds": The longest runtime in seconds for the named task
  • "stdDevRunningSeconds": The standard deviation of runtimes for the named task
  • "maximumCpuUtilizationRatio": The highest CPU utilization ratio seen for any of the named tasks
  • "meanCpuUtilizationRation": The average CPU utilization ratio for the named task
  • "maximumMemoryUtilizationRatio": The highest memory utilization ratio seen for any of the named tasks
  • "meanMemoryUtilizationRation": The average memory utilization ratio for the named task
  • "maximumGpusReserved": The largest number of GPUs reserved for the named tasks
  • "meanGpusReserved": The average number of GPUs reserved for the named task
  • "recommendedCpus": The recommended number of Cpus that would accommodate all observed instances of a task (including any headroom factor)
  • "recommendedMemoryGiB": The recommended GiBs of memory that would accommodate all observed instances of a task (including and headroom factor)
  • "recommendOmicsInstanceType": The recommended omics instance type that would accomodate all observed instances of a task
  • "maximumEstimatedUSD": The largest estimated cost observed for the named task.
  • "meanEstimatedUSD": The average estimated cost observed for the named task.

HealthOmics Run Dashboard

The run_dashboard tool builds an Amazon CloudWatch dashboard of per-workflow resource utilization from the HealthOmics vended run metrics (the aws.omics.* OpenTelemetry metrics; see https://docs.aws.amazon.com/omics/latest/dev/monitoring-run-metrics.html).

The dashboard has one row per workflow and six plots per row — CPU utilization %, memory utilization %, filesystem I/O (read/write), network I/O (receive/transmit), run shared-filesystem usage, and scratch storage usage — each plotting the average and p99 across the workflow's tasks/runs. CPU and memory utilization are computed per task (usage / limit) and then aggregated, which is correct even when a workflow's tasks request different amounts of CPU/memory. Scratch storage usage is the per-task local scratch metric (aws.omics.task.filesystem.scratch.storage.usage).

There are two ways to set the dashboard up: run the run_dashboard CLI command, or deploy the one-click CloudFormation stack described below. Both produce the same dashboard; pick whichever fits your workflow.

Example

The generated dashboard looks like this (three workflows, six plots per row):

Example HealthOmics run dashboard with one row per workflow and six plots per row

Option 1 — CLI

For an overview and the available options run:

aws-healthomics-tools run_dashboard -h

Your run service role must have cloudwatch:PutMetricData so the metrics exist. The tool only touches the single dashboard it manages — it creates/updates it (cloudwatch:PutDashboard) or deletes it (cloudwatch:DeleteDashboards, with --delete); it never creates, deletes, or modifies workflows or runs. Panel titles use the real workflow name (resolved with the read-only omics:GetWorkflow), falling back to workflow-<n> if the name cannot be resolved.

Pass the workflow ids to chart with -i. The following builds a dashboard named omics-workflow-usage in us-west-2 for two workflows:

aws-healthomics-tools run_dashboard -i 1234567,2345678 -r us-west-2 -d omics-workflow-usage

Preview the dashboard body without creating anything:

aws-healthomics-tools run_dashboard -i 1234567 --dry-run

Delete a dashboard you created (by name — no workflow ids needed):

aws-healthomics-tools run_dashboard --delete -d omics-workflow-usage -r us-west-2

Options:

  • -i, --workflow-ids — comma-separated workflow ids to chart (required unless --delete).
  • -r, --region — AWS Region (default us-west-2).
  • -d, --dashboard-name — CloudWatch dashboard name (default omics-workflow-usage).
  • --dry-run — print the dashboard body instead of creating the dashboard.
  • --delete — delete the dashboard named by --dashboard-name instead of creating it.

Option 2 — one-click CloudFormation stack

If you'd rather not install the CLI, deploy the template at cloudformation/omics-dashboard-oneclick.json. It creates a single AWS::CloudWatch::Dashboard for 1–6 workflow ids and needs no code or dependencies. Deploy it from the console (CloudFormation → Create stack → upload the template) or from the CLI:

aws cloudformation deploy \
  --template-file cloudformation/omics-dashboard-oneclick.json \
  --stack-name omics-workflow-usage \
  --parameter-overrides WorkflowId1=1234567 WorkflowId2=2345678

Parameters: DashboardName (default omics-workflow-usage), WorkflowId1 (required), and WorkflowId2–WorkflowId6 (optional; leave blank to omit a row). The stack deploys into the Region of the CloudFormation stack and outputs the dashboard console URL. Because CloudFormation does not call omics:GetWorkflow, the CloudFormation panels are titled by workflow id rather than name — the one behavioral difference from the CLI.

Security

See CONTRIBUTING for more information.

License

This project is licensed under the Apache-2.0 License.

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0.11.0

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