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Op 22 mei 2015 om 18:01 heeft "galaxy-dev-request@lists.galaxyproject.org" <galaxy-dev-request@lists.galaxyproject.org> het volgende geschreven:

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Today's Topics:

1. Re: connecting composite data elements to a display application (Brian Haas) 2. Re: connecting composite data elements to a display application (Daniel Blankenberg) 3. Re: connecting composite data elements to a display application (Brian Haas) 4. Re: samtools index tool (Eleanor Morgan) 5. Re: samtools index tool (Peter Cock) 6. Re: Web processes and SSL (John Chilton) 7. Re: error executing test (John Chilton) 8. Re: error executing test (Roberto Alonso CIPF)

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Message: 1 Date: Thu, 21 May 2015 13:48:11 -0400 From: Brian Haas <bhaas@broadinstitute.org> To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] connecting composite data elements to a display application Message-ID: <CAJCu8qObPm71Ht1QYnmLvcZB966Vp26cq8of4FxmXF7xq2uukQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

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 <bhaas@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.gruening@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>