The following slides show how my 'hack' works:

ftp://ftp.broadinstitute.org/pub/users/bhaas/tmp/FI-web.pptx

 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.

best,

~brian


On Thu, May 21, 2015 at 7:18 AM, Brian Haas <bh...@broadinstitute.org>
wrote:

> 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
> javascript version of IGV) to access and display these files.  The IGV-web
> 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
>
>     galaxy/display_applications/display.xml
>
> file to indicate how the URL should be constructed.  The final url could
> be simply:
>
>     http://MyWebServer/my_web_app.cgi?data_base_url=http://galaxyURL
>
> 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,
>
> ~brian
>
>
>
>
> 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.
>>
>> Cheers,
>> Bjoern
>>
>>
> --
> --
> Brian J. Haas
> The Broad Institute
> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
>
>
>



-- 
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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