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
_______________________________________________ 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
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. Thanks, Ed On Sun, Jul 17, 2011 at 8:39 AM, Jim Johnson <johns198@umn.edu> wrote:
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> 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> 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 http://lists.bx.psu.edu/listinfo/galaxy-dev
participants (2)
-
Edward Kirton -
Jim Johnson