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Old 03-12-2012, 07:43 PM   #1
ehlin
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Location: NYC

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Default Is it possible to run a web browser program (IMGT V-QUEST) from Unix?

I want to use IMGT V-QUEST to map VDJ regions on my Ion Torrent reads in my computer cluster.

(http://www.imgt.org/IMGT_vquest/vque...Option=humanIg)

However, V-Quest is only available through a web browser, so one solution is to transfer gigabytes of data from the cluster to my terminal PC, use the software, and then transfer it back. It would great if I could avoid this. Does anyone have any advice?

Thanks,
Edwin
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Old 03-13-2012, 12:33 AM   #2
arvid
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Did you try to do run a X-server (like Xming for Windows) on your desktop PC and tunnel X through ssh (if you're on Windows, you can configure Putty to do that)? Then you can start GUI applications (like firefox) on the Unix server and have the windows on your desktop. This requires of course that firefox is installed on the Unix server (might not be the case if it is a cluster); you could also try a text-based browser such as lynx (although most websites these days don't work very well with it).

In either case, are you sure that V-Quest is able to handle gigabytes of data in a form submission (many web applications will have problems with this)? You might need to filter your reads first to be sure only to have the relevant reads for this kind of analysis...
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Old 03-13-2012, 03:04 AM   #3
Simon Anders
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Do you mean by "only availabe through a web browser" that you have to upload your data to their server? In this case, it does not make a difference from where you upload your way-too-large data set. Or rather, that you can download the whole software but must install it at a local web server? Then, why not run server and client both on the cluster?

And just to be clear: Of course, you can run a web browser like Firefox from a node of a unix compute cluster, using X11 forwarding, as arvid said. You may just have to persuade your sysadmin to give you permission to do so.

In any case, you will likely need the help of a bioinformatician, because I cannot imagine that you could simply upload gigabytes of data to a public server, and you won't manage to set up a local server without unix experience.
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