WDL WORKSPACE

WDL Workspace solution provides a Web-based User Interface for Cromwell server.

• Launch wdl script: upload, select from library or edit wdl script, inputs and options
• Workflow execution process: observe workflow's status, inputs, outputs, logs etc

How to build WDL Workspace

Requirements

• Node.js >=6.11.5
• npm

Build configuration

During build process following env variables are used:

• WW_CROMWELL_API: url for Cromwell server's API, e.g. http://localhost:8000/api, https://some.server.com/cromwell/api
• WW_CROMWELL_EXECUTIONS_PATH_MASK: regular expression with capture group; this expression describes path to cromwell workflow's execution directory at server (/some/root/directory/cromwell-executions); capture group is used to extract relative path to workflow execution's assets (i.e. /some/root/directory/cromwell-executions/workflow/abcd1234/call-a/stdout). Default value: ^.*\\/cromwell-executions\\/(.+)$
• WW_CROMWELL_EXECUTIONS_URL: url for Cromwell server's execution folder, e.g. http://some.server.com/cromwell/executions, /executions; this variable is used with WW_CROMWELL_EXECUTIONS_PATH_MASK to generate url for downloading workflow's assets
• WW_WORKFLOWS_URL: url for pre-distributed workflows ("Workflows library")
• WW_ROUTES_CONFIG_URL: url for downloading routes.json; this file is generated automatically and contains all endpoints for GUI. Default value: /routes.json

All this variables can be set using npm run script arguments:

• --api=WW_CROMWELL_API
• --executions-path-mask=WW_CROMWELL_EXECUTIONS_PATH_MASK
• --executions-url=WW_CROMWELL_EXECUTIONS_URL
• --workflows-url=WW_WORKFLOWS_URL
• --routes-config-url=WW_ROUTES_CONFIG_URL

Build process requires WW_CROMWELL_API (or npm run script --api=...) to be set.

Build for production

To build WDL Workspace run this commands in source code directory:

$ npm install
$ npm run build

This will produce build folder with app's assets.

Build for development

To build WDL Workspace for development run this commands in source code directory:

$ npm install
$ npm run start

or if you have cromwell server running on local machine (at http://localhost:8000/api) run:

$ npm install
$ npm run start-with-local-cromwell

Open http://localhost:3000 to view it in the browser.

Documentation

• Running WDL workspace using docker