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FIRECLOUD | Doc #10860 | Method Repository

Method Repository
Dictionary | Created 2017-12-01 | Last updated 2018-05-03


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The Method Repository is a place where you can browse and export methods, method configurations, create your own privately, or publish and share with the community! This is a good place to look for best practice methods that you can use on your own data in your workspace. To learn how to export and publish, see this video tutorial.

When you find the method you need, all you have to do is export it to your workspace to start running analyses. You will have the option to export a blank configuration or select a pre-populated configuration (if available). If you use a blank configuration, you will have to fill out the inputs and (optionally outputs). In contrast, if you export a pre-populated configuration, the inputs and outputs are filled out for you, so all you have to do is export and tweak it for your use case. Exporting method configs are handy if you want to reproduce someone else's analysis or don’t know the format of the inputs.

When a method is added to the Method Repository, it automatically displays a new snapshot. This ensures that methods are never overwritten and that provenance is fully captured.

The Method Namespace acts like a folder containing methods and method configs. For example, if you add the method "myAligner" to the Method Repository under the namespace "Broad", it’s identifier would be: Broad/myAligner

Many analysts choose to put their name and/or institution in the namespace field. You can label your namespaces however you see fit, provided the chosen namespace does not already exist. Administrators may verify namespaces, which like verified twitter accounts, establish the authenticity of namespaces attached to specific organizations (e.g., Broad Institute).

You can permit others to use your namespace. This is great for labs who have multiple contributors but want people to find all of their methods under the "Miller-lab", for example.


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