Unsubscribe Verstuurd vanaf mijn iPhone > Op 22 mei 2015 om 18:01 heeft &quot;galaxy-dev-request(a)lists.galaxyproject.org&quot; <galaxy-dev-request(a)lists.galaxyproject.org&gt; het volgende geschreven: > > Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.galaxyproject.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.galaxyproject.org > > You can reach the person managing the list at > galaxy-dev-owner(a)lists.galaxyproject.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > > 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&gt; > To: galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] connecting composite data elements to a > display application > Message-ID: > <CAJCu8qObPm71Ht1QYnmLvcZB966Vp26cq8of4FxmXF7xq2uukQ(a)mail.gmail.com&gt; > 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(a)broadinstitute.org&gt; > 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(a)gmail.com&gt; 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> >