Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?

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 <johns198@umn.edu mailto:johns198@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 <johns198@umn.edu <mailto:johns198@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


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