Skip to main content

Easier way to run workflows, configurable across environments

Project description

Welcome to Janis-Runner

Build Status PyPI version

Janis. is a workflow assistant designed to make the process of building and running workflows easier.

Quick start

pip3 install janis-pipelines[runner]

You can run a workflow in CWLTool with the following command line:

janis run myWorkflow.py --engine cwltool

CLI options:

  • run - Run a janis workflow
  • watch - Watch an existing execution
  • abort - Issue an abort request to an existing execution
  • inputs - Generate an inputs file for a workflow
  • translate - Translate a workflow into CWL / WDL
  • metadata - Get the available metadata on an execution
  • version - Print the version of janis_runner

run

You can run a workflow with the run method, here's an example to run the hello world example:

janis run hello

View the help guide

positional arguments:
  workflow              Run the workflow defined in this file

optional arguments:
  -h, --help            show this help message and exit
  -n NAME, --name NAME  If you have multiple workflows in your file, you may
                        want to help Janis out to select the right workflow to
                        run
  --inputs INPUTS       File of inputs (matching the workflow) to override,
                        these inputs will take precedence over inputs declared
                        in the workflow
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        The output directory to which tasks are saved in,
                        defaults to $HOME.
  -e ENVIRONMENT, --environment ENVIRONMENT
                        Select a preconfigured environment (takes precendence
                        over engine and filescheme). See the list of
                        environments with `janis environment list`
  --engine {cromwell,cwltool}
                        Choose an engine to start
  -f {local,ssh}, --filescheme {local,ssh}
                        Choose the filescheme required to retrieve the output
                        files where your engine is located. By selecting SSH,
                        Janis will SCP the files using the --filescheme-ssh-
                        binding SSH shortcut.
  --filescheme-ssh-binding FILESCHEME_SSH_BINDING
                        Only valid if you've selected the ssh filescheme. (eg:
                        scp cluster:/path/to/output local/output/dir)
  --cromwell-url CROMWELL_URL
                        Location to Cromwell
  --validation-reference VALIDATION_REFERENCE
                        reference file for validation
  --validation-truth-vcf VALIDATION_TRUTH_VCF
                        truthVCF for validation
  --validation-intervals VALIDATION_INTERVALS
                        intervals to validate between
  --validation-fields VALIDATION_FIELDS [VALIDATION_FIELDS ...]
                        outputs from the workflow to validate
  --dryrun              convert workflow, and do everything except submit the
                        workflow
  --no-watch            Submit the workflow and return the task id
  --max-cores MAX_CORES
                        maximum number of cores to use when generating
                        resource overrides
  --max-memory MAX_MEMORY
                        maximum GB of memory to use when generating resource
                        overrides
  --hint-captureType {targeted,exome,chromosome,30x,90x,300x}
  --hint-engine {cromwell}

Configuration

It's possible to configure a number of attributes of janis.runner. You can provide a YAML configuration file in two ways:

  • CLI: --config /path/to/config.yml
  • Environment variable JANIS_CONFIGPATH=/path/to/config.yml
  • Default: $(HOME)/.janis/janis.conf - will additionally look for a config here.

Configurations aren't currently cascaded, but the intention is they will.

Options

Defaults: janis_runner/management/configuration.py

  • Config / DB directory: configDir: /path/to/configir/

    • Second priority to environment variable: JANIS_CONFIGDIR
    • Default: (HOME)/.janis/
    • Database: {configDir}/janis.db - Janis global database
  • Execution directory: executionDir

    • Second priority to environment variable: JANIS_EXCECUTIONDIR
    • Default: (HOME)/janis/execution/
  • Search paths: searchPaths

    • Will additionally add from environment variable: JANIS_SEARCHPATH
    • Default: (HOME)/janis/

Engines

There are currently 2 engines that janis.runner supports:

  1. CWLTool
  2. Cromwell

CWLTool (default)

Due to the way CWLTool provides metadata, support for CWLTool is very basic, and limited to submitting workflows and linking the outputs. It doesn't allow you to disconnect and reconnect later. It's enough as a proof of concept and for very basic workflows.

You should include the --logDebug parmeter to see the output of CWLTool.

Cromwell

Cromwell can be run in two modes:

  1. Connect to an existing instance (well supported) - include the --cromwell-url argument with the port to allow Janis.runner to correctly connect to this instance.

  2. Run and manage it's own instance. When the task is started, the process_id of the started Cromwell instance is stored in the taskdb, when the task finishes execution, the process is manually stopped. You are able to disconnect from the task, but note that the Cromwell instance will be kept running until you watch the task again, it recognises that it has finished and then manually shuts it down.

Both of these options provide reporting and progress tracking due to Cromwell's extensive metadata endpoint. The TaskID (6 hex characters) is included as a label on the workflow. You can disconnect from a job and reconnect with this TaskID through the command:

janis watch $tid

A screenshot of the running the example whole genome germline pipeline (for a targeted sample) can be found below. (All engines can support this through a generalised metadata semantic (TaskMetadata), Neither CWLTool or Toil support much polling of metadata).

Screenshot of janis progress screen

Extra Cromwell comments:

  • The TaskID is bound as a label on GCP instances (as tid, allowing you to query this information).
  • Janis uses the development spec of WDL, requiring Cromwell-42 or higher.
  • If asking Janis to start its own Cromwell instance, it requires the jar to be exported as $cromwelljar.

Environments

Environments are a combination of an Engine and a Filesystem. They save you from having to constantly specify your engine (+ parameters).

Environment information is used as a template, in which the task stores its own copy of the filesystem and engine. This was chosen as it allows a task's output to be relocated without losing workflow metadata.

Adding and deleting environments is currently UNAVAILABLE.

Actions:

  • List: janis environment list
  • Create: unavailable (proposed: janis environment create 'env' --engine 'engineId' --filescheme 'fsid')
  • Delete unavailable (proposed: janis environment -d 'env')

Filesystem

There is a weak concept of a filesystem for where your workflow is executed. This tool is really only developed for using the LocalFileSystem.

Supported filesystems:

  • LocalFileScheme
  • SSHFileScheme (identifier, connectionstring) - I'd recommend creating an SSH shortcut to avoid persisting personal details in database. Janis uses the connection string like so: scp connectionstring:/path/to/output /local/persist/path

Datbases

Janis stores a global SQLite database at {configDir}/janis.db of environments and task pointers (default: ~/.janis/janis.db). When a task is started, a database and workflow files are copied to a generated output folder (default: ~/janis/execution/{workflowName}/${yyyymmdd_hhMM}_{tid}/task.db).

v0.6.0

Version v0.6.0 brings new backwards-incompatible changes to the metadata structure, as well as significant changes to the Janis API.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for janis-pipelines.runner, version 0.6.2
Filename, size File type Python version Upload date Hashes
Filename, size janis_pipelines.runner-0.6.2-py3-none-any.whl (85.0 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size janis-pipelines.runner-0.6.2.tar.gz (53.7 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page