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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)
> Message: 1
> Date: Thu, 21 May 2015 13:48:11 -0400
> From: Brian Haas <bhaas(a)broadinstitute.org>
> To: galaxy-dev(a)lists.galaxyproject.org
> Subject: Re: [galaxy-dev] connecting composite data elements to a
> display application
> Content-Type: text/plain; charset="utf-8"
> 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 <bhaas(a)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.gruening(a)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
>>> into Galaxy and would open up your webapp also for other servers.
>> Brian J. Haas
>> The Broad Institute
> Brian J. Haas
> The Broad Institute