These are all good ideas but I don't think any of the constituent parts are currently possible (symbolic linking outside of libraries, tools that create collections, data sources that create collections, starting workflows with data source tools - there is some bug that prevents GenomeSpace from working for instance). If you are developing something from the ground up - you may want to just drive this all externally with the API - you create create library datasets that are linked, move them into a history and create a collection, send that collection into a workflow - this is all doable but would mean building an external UI for running workflows :(. Sorry I don't have better news. Would love pull requests to address some of these issues - but it is a lot of work. -John On Mon, Nov 10, 2014 at 2:29 PM, Aaron Petkau <aaron.petkau@gmail.com> wrote:

Hello,

I've been spending a bit of time looking over Data Sources for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Galaxy, along with some user credentials. In this sense it would be similar to the GenomeSpace importer tool.

However, instead of just exporting a set of files to a user's history, I'd like to be able to also automatically group these files into a dataset collection. I would also like to be able to link to these files instead of creating copies (which I think I can only do through a Data Library am I correct?). Ideally, I'd like to be able to use this tool as the first step in a workflow, which would allow me to import and structure the data needed for the rest of the workflow.

Does anyone have any experience writing a similar tool? Is this possible in the current Galaxy version?

Thanks,

Aaron

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