July 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] EpiGRAPH
by Greg Von Kuster 21 Jul '11

21 Jul '11

Hello Christoph, This is the result of a bug that I've corrected in change set 5819:0f15591f2acd, which should be available in our main Galaxy instance, as well as the distribution, within the next few weeks. Thanks for pointing this out, and very sorry for the inconvenience. Greg Von Kuster On Jul 21, 2011, at 12:58 AM, Christoph Bock wrote: > Hi Greg, Anton, > > I received a user bug report asking why the “Send Data -> EpiGRAPH” function in Galaxy doesn’t work anymore. > Is this a temporary technical issue or did you do a general cleanup and removed this link? > > Best regards, > Christoph > > From: Christoph.Schmid(a)unibas.ch [mailto:Christoph.Schmid@unibas.ch] > Sent: 13 July 2011 3:56 AM > To: cbock(a)mpi-inf.mpg.de > Subject: EpiGRAPH > > Dear Christoph, > > I am trying to get an overview on existing computational solutions in the public domain to compare epigenetic maps. > > One interesting solution is your EpiGRAPH Software (Genome Biol 10, R14.[2009]). I have the following questions: > > 1) Could I get access to the most recent source code release, & installation instructions (I saw the pre-print of the tutorial paper)? Any comments on current and future development activities on EpiGRAPH? > > 2) What is the state of the integration of EpiGRAPH into the Galaxy framework? As far as I remember EpiGRAPH was available for a short moment onhttp://main.g2.bx.psu.edu/, but now I can no longer see it? Is it still available on another mirror? > > thanks in advance for your help > ->Christoph > > ******************************************************** > Christoph D. Schmid, PhD > > Swiss Tropical and Public Health Institute > Socinstrasse 57 > CH-4002 Basel > Switzerland > > skype: chimborazo93 > Tel +41 61 284 8323 > Fax +41 61 284 8101 > > www.swisstph.ch > > > -------------------------------------------------------------------------- > This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error, please notify us immediately by reply e-mail and delete this message from your system. > -------------------------------------------------------------------------- Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Best location for galaxy environmental variables
by michael burrell (TSL) 21 Jul '11

21 Jul '11

Good afternoon, More of a general discussion point, where is the best place to put the environmental variable declarations within galaxy. To date I have been placing them as exports in the run.sh, though I can not help but wonder if there is a better place, which is appropriate whatever method you use to kick off galaxy. Thanks Michael.

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Newer Version of Cufflinks Wrapper
by Chorny, Ilya 20 Jul '11

20 Jul '11

Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Error in exporting workflow
by chan fook mun 19 Jul '11

19 Jul '11

Hi All, I have encountered the following error (image attachment) when i try to export a workflow: No JSON object could be decoded: line 1 column 0 (char 0) I try to google but to no avail. I wonder if anyone has encountered similar problems before. Regards, Chan Fook Mun

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use remote data without duplication
by Caroline Prenoveau 19 Jul '11

19 Jul '11

Hi, We are a small lab and we would like to use galaxy to do our analysis. However we have a very large amount of data that is stored on several machines and that we cannot afford to duplicate. Our galaxy server is set up on a different machine. We are looking for a way to use our remote data inside galaxy without copying it locally. Any ideas/hints? Thanks, Caroline

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Pull request for Galaxy
by Nick Semenkovich 19 Jul '11

19 Jul '11

Hi -- I just submitted a tiny first pull request for some minor Galaxy changes (to correct wiki links): https://bitbucket.org/galaxy/galaxy-central/pull-request/2/update-galaxy-wi… (Not sure if I should e-mail the dev list about these or what. How do these get approved?) Thanks! Nick -- Nick Semenkovich 314.374.4434 Medical Scientist Training Program School of Medicine Washington University in St. Louis http://web.mit.edu/semenko/

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Re: [galaxy-dev] fyi: can't upload to toolshed
by Greg Von Kuster 19 Jul '11

19 Jul '11

Hello Ed, This one was tough to track down, but I believe I have it resolved. On Linux, the mercurial api's call to commit seems to bump into issues intermittently, throws an exception, and rolls back the transaction. Although I can reproduce it on Linux, I cannot produce this behavior on a Mac. I've added exception handling in the latest version of the tool shed that uses a different approach to committing the changes whenever the intermittent exception is thrown. Thanks for finding this issue, and please let me know if you bump into any problems in the future. Greg Von Kuster On Jul 15, 2011, at 1:20 PM, Edward Kirton wrote: > it was for an upload of MUSCLE. the error only occurred when i uploaded the XML file uncompressed. it worked fine later when i put it in a tarball. > > On Fri, Jul 15, 2011 at 6:48 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Ed, > > Looking at the logs, I see that you uploaded to your Roche454 tool suite repo. Is that correct? I don't see any exceptions in the logs, so not sure what happened. Are you still having this issue? > > Thanks, > > Greg Von Kuster > > On Jul 14, 2011, at 9:32 PM, Edward Kirton wrote: > >> Server Error >> >> An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > Greg Von Kuster > Galaxy Development Team > greg(a)bx.psu.edu > > > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Fwd: Status of Job after log out
by shashi shekhar 19 Jul '11

19 Jul '11

---------- Forwarded message ---------- From: shashi shekhar <meshashi29(a)gmail.com> Date: Tue, Jul 19, 2011 at 3:41 PM Subject: Status of Job after log out To: shashi shekhar <meshashi29(a)gmail.com> Hi all, I took one job which takes long time to run . In galaxy, this job was submitted . After log out from galaxy ,job was running . After login again ,i checked the status of job . It showed running . How is it implemented in galaxy ? Regards shashi shekhar

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Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?
by Jim Johnson 19 Jul '11

19 Jul '11

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(a)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(a)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(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> > >

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checkers
by SHAUN WEBB 18 Jul '11

18 Jul '11

Hi, I recently update to the latest dist release and I'm getting this error whenever I try to upload files Traceback (most recent call last): File "/storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py", line 11, in from galaxy.datatypes.checkers import * ImportError: No module named checkers Should this module be provide with Galaxy or do I have to download it from somewhere? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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