[galaxy-dev] Sourcing Files from Datasets

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[galaxy-dev] Sourcing Files from Datasets

Dennis Gascoigne-2
We have put together a stack of our standard workflows in Galaxy and it is working well. Thanks.

One feature that would be infiinitely useful - i.e. we would be using it now, would be the ability to source files from the data libraries. We know you can add an item to the history thourgh the data libraries interface, but having an input tool, and.or being able to select an input from the data libraries when using the workflow designer would be great.

If this is ont something you are keen on, any pointers on the best way to implement this - i have some ideas but have no idea if they are the best way.

Cheers
Dennis


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Re: [galaxy-dev] Sourcing Files from Datasets

Jeremy Goecks
Hi Dennis,

We've gotten this request from a number of people, and it's definitely high on our list of enhancements. We've also created an issue for it, so you can follow or comment on it:


I'm not sure when we're going to get to this, so you may want to consider implementing it yourself. If you were to implement it yourself, I'd suggest the following approach:

*modify the workflow UI to include a data library as input (modify the workflow tool panel and workflow Javascript);
*(maybe) modify the workflow controller to accept/store data library types as inputs;
*modify the "run workflow" page so that a user can select a library rather than a dataset;
*modify the run workflow code to iterate over the library and run the workflow multiple times.

The good news is that many/all of these modifications can be made by altering/building on current code rather than developing significantly new code/data structures. If you do end up implementing this feature, please send us a patch and we'll try to integrate it into the code base.

Hope this helps,
J.



On Jun 1, 2010, at 6:09 AM, Dennis Gascoigne wrote:

We have put together a stack of our standard workflows in Galaxy and it is working well. Thanks.

One feature that would be infiinitely useful - i.e. we would be using it now, would be the ability to source files from the data libraries. We know you can add an item to the history thourgh the data libraries interface, but having an input tool, and.or being able to select an input from the data libraries when using the workflow designer would be great.

If this is ont something you are keen on, any pointers on the best way to implement this - i have some ideas but have no idea if they are the best way.

Cheers
Dennis

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