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.
On Mon, Nov 10, 2014 at 2:29 PM, Aaron Petkau <aaron.pet...@gmail.com> wrote:
> 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?
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: