- galaxy-dev - lists.galaxyproject.org

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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Multiple fastq files per forward/reverse mates (tophat and related tools)
by W. Augustine Dunn III 15 Jul '11

15 Jul '11

I want to customize the tophat and related interfaces to allow more than one fastq file per fwd/rev set as is allowed and very helpful in the CLI version: $ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq Is there a way to select multiple items from a dropdown menu or can/should i convert that part of the interface to a text input field so I can simply feed the command a list of files like on the command line? This last method seems like it might be a little unsafe though. But even if its not, it divorces the file management from the history which seems like its not a good idea. Has anyone done this? Thanks, Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould*

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fyi: can't upload to toolshed
by Edward Kirton 15 Jul '11

15 Jul '11

Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here)

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Sending Data to Galaxy
by Amirhossein Kiani 14 Jul '11

14 Jul '11

Hey Galaxy developers! I was wondering if anyone knows how to send data to a local galaxy instance from another server (I'm interested in sending a BAM file to Galaxy). I see that UCSC and others have done it but couldn't find anything about the API doc they are using... Looking at the request headers from UCSC, I see that this request: tool_id:bx_browser URL:http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables hguid:883956 db:hg18 org:Human hgta_table:seq hgta_track:gold hgta_regionType:genome hgta_outputType:primaryTable position:chr10:90997300-90997350 hgta_doTopSubmit:get output hgsid:62857 hgta_doGalaxyQuery:Send query to Galaxy has been sent to: http://main.g2.bx.psu.edu/tool_runner Is this all needed? If so how is the URL to the data file passed to Galaxy? Many thanks! Amir

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more cleanup scripts messages
by Assaf Gordon 14 Jul '11

14 Jul '11

Hi Greg (again), This patch adds messages for the "purge histories" step: 1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong). 2. in "info_only" mode, a message is printed about each deleted history 3. in "info_only" mode, a message is printed for each HDA that is checked 4. The message for HDA is changed to include the associated dataset id. Comments are welcomed, -gordon

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Saved Histories - default view on deleted histories (bug)
by Michal Stuglik 14 Jul '11

14 Jul '11

hi all, in galaxy-central: 1. default view in "Saved Histories" section is set on deleted items ( Jeremy, I did double check this morning on fresh instance :)) 2. in advanced search option: one of the filter switch is deleted and does the same job as active switch 3. Sugestion: Saved Histories->Advanced Search sharing: private | shared | accessible | published | all deleted: active | deleted | all maybe it is better to change it to: sharing: private | shared | accessible | published | all status: active | deleted | all I think "deleted" is not clear.. all the best, michal

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toolExample.pl script bug report
by Casey Bergman 14 Jul '11

14 Jul '11

Dear Galaxy Team - We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences. If you could confirm this and modify if possible, this might help other users. All the best, Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman Email: casey.bergman(a)manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/

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Possible to re-use toolconfig xml files outside Galaxy?
by Samuel Lampa 14 Jul '11

14 Jul '11

Hi, I have been looking into re-using the galaxy toolconfig xml files outside galaxy, for auto-generating wizards for command line tools, in an own little (eclipse based) software (For a short background, see [1]). I have come to realize though that the xml-files are not really independent, but (almost?) always is accompanied by a correpsonding .py file, which does more or less tricks, which seemingly makes it very hard to use the xml-files outside a galaxy/python environment at all. My questions: 1. Are the xml-files *always* accompanied by the .py file, or is that optional? 2. Would my idea be possible/reasonable at all? 3. Are there other more general tool config formats that I could use, since I'm not using galaxy atm? 4. Any other suggestions or ideas? Best Regards // Samuel [1]: The tool is built as a complement to some galaxy initiatives at the UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to configure batch scripts for the software installed at UPPMAX, of which bioinformatics tools are just a part. The galaxy toolconfig xml-format looked useful though, and seemed to enable us to have at least most of our bioinformatics tools (the category with most installed tools at UPPMAX) already configured. -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa(a)scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se

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