Ed,
I pushed what code I had to the toolshed repository "qiime" and gave you push permissions. I'm not sure when I'll have time to work on it again. Thanks, JJ On 7/15/11 3:18 PM, Edward Kirton wrote:
fantastic, thanks! i'm also available to help out, so perhaps you can find me something to work on. ed On Fri, Jul 15, 2011 at 1:09 PM, Jim Johnson <johns...@umn.edu <mailto:johns...@umn.edu>> wrote: I haven't had time to work on it for a couple months. I remember getting stuck on the output of some scripts being a HTML with a file hierarchy underneath. I proposed setting the galaxy routes to accept those, and that has since been incorporated. I'll try to do a run through of what I had, and update what was working to the current galaxy-central tip. Then, maybe I'll bundle that and put it in the toolshed for common development. Does that work for you? Thanks, JJ On 7/15/11 1:58 PM, Edward Kirton wrote:Hello James, I was wondering if you're still tackling the task of adding QIIME to galaxy? I have some users in my group asking about this and I'd rather not duplicate any efforts. If you're still working on this, do you have a ballpark estimate of when this will appear in the toolshed? Many thanks, Ed Kirton US DOE JGI (http://galaxy.jgi-psf.org) p.s. great job on the mothur suite; thanks! i just found it in the toolshed yesterday. On Wed, Nov 24, 2010 at 7:31 AM, Jim Johnson <johns...@umn.edu <mailto:johns...@umn.edu>> wrote: Tim, I hope to also look at incorporating QIIME into our local Galaxy instance at the University of Minnesota, but probably won't be able to start for a couple weeks. It would be good to develop that in coordination with others. I just finished incorporating "Mothur" metagenomics suite http://www.mothur.org/ (Dr. Patrick Schloss, Department of Microbiology & Immunology at The University of Michigan) into our Galaxy server at the University of Minnesota. I hope to contribute that to http://community.g2.bx.psu.edu/ after some testing by our researchers. If the Galaxy wrappings for Mothur are of any interest to you, I can send you a copy any time. Thanks, JJ James E Johnson Minnesota Supercomputing Institute University of Minnesota On Nov 23, 2010 at 07:22 AM, Tim te Beek wrote: Hello all, Is anyone aware of any existing efforts to port the QIIME sequencing pipeline (http://qiime.sourceforge.net/) to Galaxy? I would like to run QIIME analyses through Galaxy to get better control of intermediate processing steps, but before I start to convert (a subset of) some 90 scripts, I'd first like to make sure this has not been done before by anyone willing to share their work. So: has anyone converted the QIIME pipeline to Galaxy before, and would they be willing to share their scripts? Best regards, Tim _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-dev
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