Re: [galaxy-user] [Gmod-help] GMOD and Galaxy
Hi Rashad, GBrowse is currently the only other GMOD component that Galaxy talks to. There has been discussion in the past about getting it work with Chado as well, but there hasn't yet been sufficient interest to justify that work. I'm forwarding this e-mail to the Galaxy-user list in case I'm wrong about that. Documentation on how to get Galaxy and GBrowse to talk with one another is at: http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options There may be more doc at the Galaxy web site. Please let me know if this does not answer your questions. Regards, Dave C. GMOD Help Desk Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback On Tue, Mar 17, 2009 at 2:54 PM, Rashad Arafeh <arafeh@gmail.com> wrote:
hello,
My name is Rashad Arafeh, I just recently graduated in Computer Science, and have been encouraged to look into a career in Bioinformatics and Computational BIology.
I am volunteering to help a professor at the University of Texas - Arlington set up his lab with some bioinformatics tools that he thinks are necessary, and from there i will begin to solve some bioinformatics problems with him.
Since we are both new to GMOD and its components, we are pretty much learning as we go, but he has it clear in his mind that he wants "in-house" functionality similar to that of the UCSC Genome Browser and Galaxy system.
My questions are:
-I noticed that Galaxy is listed as a GMOD component, and i want to downlaod and install it and have it run locally, how do i get it to interact with GBrowse and other components?
-What set of components, if there are any, would give me functionality similar to that of UCSC Genome Browser with Galaxy?
Thank you, Rashad Arafeh
Hello Rashad, The Galaxy download is fully integrated with Biomart, Flymine, Wormbase, and can easily be integrated with other external data sources. Integrating a new external data source into your Galaxy instance is as simple as copying one of the existing data source tool config files and editing the tags to point to the new data source. For more information about integrating new data sources, see http://g2.trac.bx.psu.edu/wiki/DataSources. Please let me know if you have any questions as you work with Galaxy. Thanks very much, Greg Von Kuster Galaxy Development Team Dave Clements, GMOD Help Desk wrote:
Hi Rashad,
GBrowse is currently the only other GMOD component that Galaxy talks to. There has been discussion in the past about getting it work with Chado as well, but there hasn't yet been sufficient interest to justify that work. I'm forwarding this e-mail to the Galaxy-user list in case I'm wrong about that.
Documentation on how to get Galaxy and GBrowse to talk with one another is at: http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options
There may be more doc at the Galaxy web site.
Please let me know if this does not answer your questions.
Regards,
Dave C. GMOD Help Desk
Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
On Tue, Mar 17, 2009 at 2:54 PM, Rashad Arafeh <arafeh@gmail.com> wrote:
hello,
My name is Rashad Arafeh, I just recently graduated in Computer Science, and have been encouraged to look into a career in Bioinformatics and Computational BIology.
I am volunteering to help a professor at the University of Texas - Arlington set up his lab with some bioinformatics tools that he thinks are necessary, and from there i will begin to solve some bioinformatics problems with him.
Since we are both new to GMOD and its components, we are pretty much learning as we go, but he has it clear in his mind that he wants "in-house" functionality similar to that of the UCSC Genome Browser and Galaxy system.
My questions are:
-I noticed that Galaxy is listed as a GMOD component, and i want to downlaod and install it and have it run locally, how do i get it to interact with GBrowse and other components?
-What set of components, if there are any, would give me functionality similar to that of UCSC Genome Browser with Galaxy?
Thank you, Rashad Arafeh
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participants (2)
-
Dave Clements, GMOD Help Desk -
Greg Von Kuster