Genomespace Integration with workflows

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Genomespace Integration with workflows

Nuwan Goonasekera

This is with regard to a modification we'd like to propose for improving Genomespace integration with Galaxy, and we'd like to get some feedback from the core Galaxy devs. We are happy to make the changes and issue a pull request.

The proposal is:
1. Allow the Genomespace Importer to be workflow compatible (that is, allow the Genomespace Importer to be dragged/dropped onto the workflow canvas and when the user attempts to run the workflow, provide a way to specify/browse for a file stored in Genomespace through a popup window)

2. Do the same for the Genomespace Exporter, so that, at the end of running a workflow, the file would be archived back in Genomespace automatically.

So far, the only solid approach we've found to implement this is to introduce a new tool parameter (e.g. GenomespaceFileParameter, analogous to FtpFileParameter). It removes many of the constraints that the current genomespace import/export tools are bound by. It may also necessitate the inclusion of some javascript so that the file browse dialogue can be opened.

Alternatively, it could be made more generic, e.g. CustomFileParameter instead of GenomespaceFileParameter - with a property for specifying a custom javascript handler. However, since tools do not appear to have a way of introducing custom javascript code at present, this approach may not be viable.

So we were wondering whether the initial approach was alright or whether there's a better method of achieving this?


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