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>
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