I took a look and it's a great start. I can work on it 1d/wk. I'll email
you again after I push my revisions to the toolshed. Or email me anytime
you want me to push whatever I've got at that time.
On Sun, Jul 17, 2011 at 8:39 AM, Jim Johnson <johns...@umn.edu> wrote:
> 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.
> 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> 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> 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 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.
>>> 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
>>>> 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
>>>> be willing to share their scripts?
>>>> Best regards,
>>> galaxy-dev mailing list
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