Bed-To-Gff: Option For Gff3 Format

7.7 years ago by

Karen Tang • 40 wrote:

Hi Galaxy developers, Any plans on adding a GTF-to-GFF3 format conversion? This converter is at the Rätsch lab's instance of Galaxy (http://galaxy.tuebingen.mpg.de/). Could it be made more widely available? Karen :) Dept of Plant Biology University of Minnesota

ADD COMMENT • link written 7.7 years ago by Karen Tang • 40

Hey guys, Is there an irc channel for galaxy? I googled for "galaxy irc" but all I see in the first fifty results are entries for the samsung galaxy (which is an excellent phone ;) Best Regards, George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a

ADD REPLY • link written 7.7 years ago by George Marselis • 10

Hi George, Thanks to your suggestion and work by Nate Coraor, Galaxy now has an IRC channel: Server: irc.freenode.net Channel: #galaxyproject This is an informal online gathering place for the Galaxy community to post questions and help each other out. Note that while IRC is conducive to quick discussion, it doesn't work so well as an official support channel (and therefore IRC is not an official Galaxy support channel). If you have a question, bug, or feature suggestion that you want to make sure the Galaxy team knows about, please continue to send these to the mailing lists. Please reply to this thread if you have any questions, or you can post them on the IRC. Thanks, Dave C. On Mon, Mar 7, 2011 at 1:57 PM, George Marselis < -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

ADD REPLY • link written 7.7 years ago by Dave Clements ♦♦ 2.5k

Karen, Sorry for the slow reply. There are no immediate plans to add either BED-to-GFF3 or GTF-to-GFF3 converters to Galaxy main or the Galaxy codebase. However, if you're working with your own Galaxy, you might encourage the Rätsch lab to contribute their tools to the Galaxy Tool Shed (http://community.g2.bx.psu.edu/); you could then download them from there and install them in your own Galaxy. Alternatively, we welcome community contributions to the Galaxy codebase, and we'd be happy to incorporate these tools if they came with functional tests and test data. Best, J.

ADD REPLY • link written 7.7 years ago by Jeremy Goecks • 2.2k

Speaking of which, could a Galaxy developer look at adding these changes, please? https://bitbucket.org/galaxy/galaxy-central/issue/447/new-tools-to-de- interlace-fastq-mate-pair Thanks, Florent

ADD REPLY • link written 7.7 years ago by Florent Angly • 370

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