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webgme/webgme-cwl

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webgme-cwl

Installation

First, install the webgme-cwl following:

Second, start mongodb locally by running the mongod executable in your mongodb installation (you may need to create a data directory or set --dbpath).

Then, run webgme start from the project root to start . Finally, navigate to http://localhost:8888 to start using webgme-cwl!

Step usage guide

Generic

The following rules are for most steps and how they are handling inputs and outputs.

  • by default any input will be passed to the command and the prefix will be the name of the port (with '--')
  • if you do not want to pass an input to the command, you need to set inside the input's config the 'skip field to true
  • also if you do need the that given input you need to use the input config copyTo field and add a path relative to the execution directory

DockerStep

This step is trying to simplify the execution of any docker based command. The following parameters will complete the step and allow for fine-tuning.

  • in the step's config, you can pass any of the 'docker...' fields (dockerPull, etc.) and they will be passed to the CWL files docker requirement as-is.
  • this step also uses the config's 'baseCommand' field and use it as-is

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