{ "info": { "author": "Michael Franklin", "author_email": "michael.franklin@petermac.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering" ], "description": "# Welcome to Janis-Runner\n\n[![Build Status](https://travis-ci.org/PMCC-BioinformaticsCore/janis-runner.svg?branch=master)](https://travis-ci.org/PMCC-BioinformaticsCore/janis-runner)\n[![PyPI version](https://badge.fury.io/py/janis-pipelines.runner.svg)](https://badge.fury.io/py/janis-pipelines.runner)\n\n[Janis](https://github.com/PMCC-BioinformaticsCore/janis). is a workflow assistant designed \nto make the process of building and running workflows easier. \n\n## Quick start\n\n```bash\npip3 install janis-pipelines[runner]\n```\n\nYou can run a workflow in CWLTool with the following command line: \n```bash\njanis run myWorkflow.py --engine cwltool\n```\n\n## CLI options:\n\n- `run` - Run a janis workflow\n- `watch` - Watch an existing execution\n- `abort` - Issue an abort request to an existing execution\n- `inputs` - Generate an inputs file for a workflow\n- `translate` - Translate a workflow into CWL / WDL\n- `metadata` - Get the available metadata on an execution\n- `version` - Print the version of `janis_runner`\n\n### `run`\n\nYou can run a workflow with the `run` method, here's an example to run the hello world example:\n\n```bash\njanis run hello\n```\n\nView the help guide \n\n```\npositional arguments:\n workflow Run the workflow defined in this file\n\noptional arguments:\n -h, --help show this help message and exit\n -n NAME, --name NAME If you have multiple workflows in your file, you may\n want to help Janis out to select the right workflow to\n run\n --inputs INPUTS File of inputs (matching the workflow) to override,\n these inputs will take precedence over inputs declared\n in the workflow\n -o OUTPUT_DIR, --output-dir OUTPUT_DIR\n The output directory to which tasks are saved in,\n defaults to $HOME.\n -e ENVIRONMENT, --environment ENVIRONMENT\n Select a preconfigured environment (takes precendence\n over engine and filescheme). See the list of\n environments with `janis environment list`\n --engine {cromwell,cwltool}\n Choose an engine to start\n -f {local,ssh}, --filescheme {local,ssh}\n Choose the filescheme required to retrieve the output\n files where your engine is located. By selecting SSH,\n Janis will SCP the files using the --filescheme-ssh-\n binding SSH shortcut.\n --filescheme-ssh-binding FILESCHEME_SSH_BINDING\n Only valid if you've selected the ssh filescheme. (eg:\n scp cluster:/path/to/output local/output/dir)\n --cromwell-url CROMWELL_URL\n Location to Cromwell\n --validation-reference VALIDATION_REFERENCE\n reference file for validation\n --validation-truth-vcf VALIDATION_TRUTH_VCF\n truthVCF for validation\n --validation-intervals VALIDATION_INTERVALS\n intervals to validate between\n --validation-fields VALIDATION_FIELDS [VALIDATION_FIELDS ...]\n outputs from the workflow to validate\n --dryrun convert workflow, and do everything except submit the\n workflow\n --no-watch Submit the workflow and return the task id\n --max-cores MAX_CORES\n maximum number of cores to use when generating\n resource overrides\n --max-memory MAX_MEMORY\n maximum GB of memory to use when generating resource\n overrides\n --hint-captureType {targeted,exome,chromosome,30x,90x,300x}\n --hint-engine {cromwell}\n```\n\n## Configuration\n\nIt's possible to configure a number of attributes of `janis.runner`. \nYou can provide a YAML configuration file in two ways:\n\n- CLI: `--config /path/to/config.yml`\n- Environment variable `JANIS_CONFIGPATH=/path/to/config.yml`\n- Default: `$(HOME)/.janis/janis.conf` - will additionally look for a config here.\n\n> Configurations aren't currently cascaded, but the intention is they will.\n\n### Options\n\nDefaults: [`janis_runner/management/configuration.py`](https://github.com/PMCC-BioinformaticsCore/janis-runner/blob/master/janis_runner/management/configuration.py#L68)\n\n- Config / DB directory: `configDir: /path/to/configir/`\n - Second priority to environment variable: `JANIS_CONFIGDIR`\n - Default: `(HOME)/.janis/`\n - Database: `{configDir}/janis.db` - Janis global database\n\n- Execution directory: `executionDir`\n - Second priority to environment variable: `JANIS_EXCECUTIONDIR`\n - Default: `(HOME)/janis/execution/`\n\n- Search paths: `searchPaths`\n - Will additionally add from environment variable: `JANIS_SEARCHPATH`\n - Default: `(HOME)/janis/`\n\n\n## Engines\n\nThere are currently 2 engines that `janis.runner` supports:\n\n1. CWLTool\n2. Cromwell\n\n### CWLTool (default)\n\nDue to the way CWLTool provides metadata, support for CWLTool is very basic, and limited to submitting \nworkflows and linking the outputs. It doesn't allow you to disconnect and reconnect later. It's enough \nas a proof of concept and for very basic workflows. \n\nYou should include the `--logDebug` parmeter to see the output of CWLTool. \n\n### Cromwell\n\nCromwell can be run in two modes:\n\n1. Connect to an existing instance (well supported) - include the `--cromwell-url` argument with the port to \n allow Janis.runner to correctly connect to this instance.\n\n2. Run and manage it's own instance. When the task is started, the `process_id` of the started Cromwell instance\n is stored in the `taskdb`, when the task finishes execution, the process is manually stopped. You are able to\n disconnect from the task, but note that the Cromwell instance will be kept running until you `watch` the task\n again, it recognises that it has finished and then manually shuts it down.\n\nBoth of these options provide reporting and progress tracking due to Cromwell's extensive metadata endpoint. The TaskID\n(6 hex characters) is included as a label on the workflow. You can disconnect from a job and reconnect with this TaskID\nthrough the command:\n\n```bash\njanis watch $tid\n``` \n\nA screenshot of the running the example [whole genome germline pipeline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines)\n (for a targeted sample) can be found below. (All engines can support this through a generalised metadata semantic (`TaskMetadata`),\n Neither CWLTool or Toil support much polling of metadata).\n\n> ![Screenshot of janis progress screen](resources/metadata-progress.png)\n\nExtra Cromwell comments:\n\n- The TaskID is bound as a label on GCP instances (as `tid`, allowing you to query this information).\n- Janis uses the development spec of WDL, requiring Cromwell-42 or higher.\n- If asking Janis to start its own Cromwell instance, it requires the jar to be exported as `$cromwelljar`.\n\n\n## Environments\n\nEnvironments are a combination of an Engine and a Filesystem. They save you from having to constantly specify your\nengine (+ parameters).\n\nEnvironment information is used as a template, in which the task stores its own copy of the filesystem and engine.\nThis was chosen as it allows a task's output to be relocated without losing workflow metadata.\n\n> Adding and deleting environments is currently UNAVAILABLE.\n\nActions:\n\n- List: `janis environment list`\n- Create: _unavailable_ (proposed: `janis environment create 'env' --engine 'engineId' --filescheme 'fsid'`)\n- Delete _unavailable_ (proposed: `janis environment -d 'env'`)\n\n### Filesystem\n\nThere is a weak concept of a filesystem for where your workflow is executed. This tool is really only developed\nfor using the `LocalFileSystem`.\n\nSupported filesystems:\n\n- LocalFileScheme\n- SSHFileScheme (`identifier`, `connectionstring`) - I'd recommend creating an \n [SSH shortcut](https://scotch.io/tutorials/how-to-create-an-ssh-shortcut) to avoid persisting personal details in\n database. Janis uses the connection string like so: `scp connectionstring:/path/to/output /local/persist/path`\n\n\n## Datbases\n\nJanis stores a global SQLite database at `{configDir}/janis.db` of environments and task pointers \n(default: `~/.janis/janis.db`). 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