The following slides show how my 'hack' works:
It's definitely suboptimal, but at the very least, I've got something that
works and meets my immediate needs.
I'm still *very* interested in following up with an alternative that
somehow leverages a galaxy API or well-supported mechanism for doing this.
On Thu, May 21, 2015 at 7:18 AM, Brian Haas <bh...@broadinstitute.org>
> Hi Bjoern,
> My galaxy/database/files/000/dataset_1_files/ directory contains a bunch
> of files that I want to load into a genome viewer, including the target
> fasta file, .fai, several bam and .bam.bai files, and some bed files among
> a few others. I'm looking to wire up an IGV-web application (a pure
> app just needs the URLs to access these files. I have a tool built into
> galaxy that generates these files and stores them as the composite data
> type, and I'm trying to add in the visualization capability such that one
> can click on a hyperlink provided in the finished job panel in order to
> access the igv-web view.
> Again, the general issue is just - how to best enable an external
> application to access the extra_files of a composite data set?
> Ideally, it would involve configuration of some
> file to indicate how the URL should be constructed. The final url could
> be simply:
> where data_base_url just gives the base URL to where my files would exist
> on galaxy, and since I know ahead of time the names of the files to expect
> in that directory, my web app can just reconstruct the URLs to the various
> files (fa, bam, bed, etc.).
> Alternatively, the url could provide a list of urls to all of the required
> resources - with the requirement that the .bam.bai files can be accessed by
> simply putting a .bai on the end of the bam url for each bam, and likewise
> for .fai for fasta files.
> many thx,
> On Thu, May 21, 2015 at 4:56 AM, Bjoern Gruening <
> bjoern.gruen...@gmail.com> wrote:
>> Hi Brian,
>> sorry to be so late to this adventure ...
>> Can you give me a few more details about your web-application?
>> Have you considered to use the VIS framework from Galaxy or the
>> interactive environment framework?
>> This will give you more control over your datasets, because it's build-in
>> into Galaxy and would open up your webapp also for other servers.
> Brian J. Haas
> The Broad Institute
> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
Brian J. Haas
The Broad Institute
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: