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.pet...@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 > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
