I pushed what code I had to the toolshed repository "qiime"  and gave you push 
I'm not sure when I'll have time to work on it again.



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.

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 

    Does that work for you?



    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:


        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 

        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.



        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 
            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 
            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,

        galaxy-dev mailing list
        galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>

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