July 2006 - galaxy-user - lists.galaxyproject.org

some questions
by Iris Vargas Jentzsch 25 Aug '06

25 Aug '06

Dear GalaxyTeam members, I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows? And a curiosity: where are the files from the history saved? What is the size limit for all the history files? Many thanks for your cool tool! Iris ====================================== Iris M. Vargas Jentzsch PhD Student School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 (7048) e-mail: imj15(a)student.canterbury.ac.nz

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Fwd: Fwd: Galaxy2.2 Test retrieving DNA sequences
by Laura Elnitski 31 Jul '06

31 Jul '06

Hi- thanks for all of the suggestions- so far we've had no luck in obtaining our sequences. One thing I remember is that different browsers have different settings for how long they take until they time-out- maybe we should try something other than Safari? Laura Begin forwarded message: > From: "Yang, Mary \(NIH/NHGRI\) [F]" <yangma(a)mail.nih.gov> > Date: July 28, 2006 2:45:22 PM EDT > To: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov> > Subject: Re: [Galaxy-user] Fwd: Galaxy2.2 Test retrieving DNA > sequences > > Laura: > Ben and I tried the suggested options, none of them work. Also Ben > tried the other ways, like curl, did not work either. > > Mary > >

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test galaxy not working
by Ross Hardison 29 Jul '06

29 Jul '06

I only get errors when I try to load in data to http://test.g2.bx.psu.edu/ Attempt to upload a file gives: An error occurred running this job: upload failed, the url specified is invalid or you have not specified a file delete Attempt to get data from UCSC gives: An error occurred running this job: ERROR: Attempt to get ENCODE data from Galaxy gives: An error occurred running this job: ERROR: Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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Fwd: Galaxy2.2 Test retrieving DNA sequences
by Laura Elnitski 28 Jul '06

28 Jul '06

More- continued from Thursday's message: The error we receive has to do with receiving the data that Galaxy is trying to send. Is there another way to retrieve the data? We cannot display it to screen either. Is has something to do with the time-out settings on our browser, right? Thanks very much, Laura Begin forwarded message: > From: "Yang, Mary \(NIH/NHGRI\) [F]" <yangma(a)mail.nih.gov> > Date: July 28, 2006 10:39:43 AM EDT > To: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov> > Subject: Galaxy2.2 Test retrieving DNA sequences > > Laura: > Here is the message I got when I tried to save or display > the file. > > > Network Error (tcp_error) > > A communication error occurred: "" > The Web Server may be down, too busy, or experiencing other > problems preventing it from responding to requests. You may wish to > try again at a later time. > > I think the file is too large to get it through internet. It > will be nice if they could zip the file and send it. > Thank you very much. > > Mary > >

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galaxy page load failure
by Erika 28 Jul '06

28 Jul '06

Hi, Yogeshwar and I in Kateryna Makova's lab have both had trouble loading the galaxy main page http://main.g2.bx.psu.edu/ from Mueller Bldg. I was successfully using galaxy2.2 and first had trouble yesterday afternoon, Thursday July 27. The browser won't refresh or load the page. I tried using Safari 2.0.4 and internet explorer 5.2.3. Just wanted to check... Thanks for your help! erika ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185

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retrieving DNA sequences
by Laura Elnitski 28 Jul '06

28 Jul '06

Hi- We've hit a problem trying to download sequence from Galaxy. Did we ask for too many? We can't display them nor can we save them, but the query seems to have run fine. It reports 39,000 results. The data are on the test browser- id 24081. Thanks, Laura Laura Elnitski, Ph.D. Head Genomic Functional Analysis Section Genome Technology Branch National Human Genome Research Institute National Institutes of Health 5625 Fishers Lane, Rm. 5N-01R Rockville, MD 20852 phone: 301-451-0265 fax: 301-435-6170

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Windows XP instalation problem
by tras sdzd 19 Jul '06

19 Jul '06

Hi there, I have been following the instructions from the website (http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/HowToInstall) until I encountered the following problems: 1 There was missing file named universe.conf.sample but there was universe_wsgi.ini.sample. I renamed it together with the rest to universe.conf ( after that I tried and universe_wsgi.conf) 2. When I tried to run python universe_wsgi.py I've got something like - please see the attached jpeg file. Please can somebody help me with advice. Thanks in advance Reymon --------------------------------- Try the all-new Yahoo! Mail . "The New Version is radically easier to use" The Wall Street Journal

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how to share the history?
by Ying Zhang 17 Jul '06

17 Jul '06

Hi, all, Today, Ross and I tried to share our histories. And Ross told me, he had made his history accessible to me. I assume here when somebody made his history shared with me, I would automatically receive an email containing the link of the shared page. But in fact, I have not received such an email by now, one hour later than Ross shared his history. So could someone give me some instructions on how to access a shared history? Best, Ying By the way, I tried to share my history with Ross, but seems rch8(a)psu.edu is not a valid user. I am wondering when you update Galaxy to version 2.2, have you also transferred the user registrations to the new version? Because the first time I used Galaxy 2.2, I need re-register for myself again. Another concern is that Galaxy 2.2 should be our best galaxy up to now. So why don't we update the link in UCSC table browser? Yesterday, when I asked a result from table browser to be reported to galaxy, I was re-directed to the oldest galaxy1.

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Re: [Galaxy-user] Problem with intersect (bx)
by Ross Hardison 13 Jul '06

13 Jul '06

Sure. The two data files are: http://test.g2.bx.psu.edu/display?id=23602 http://test.g2.bx.psu.edu/display?id=23607 On Jul 13, 2006, at 10:33 AM, Anton Nekrutenko wrote: > Ross: > > Thanks, could you provide links to the data files by clicking on > display link and "Copy Link Location" (as shown below). > > <Picture 1.png> > > anton > > > > Anton Nekrutenko > Assistant Professor > Department of Biochemistry and Molecular Biology > Center for Comparative Genomics and Bioinformatics > 505 Wartik Building > PennState University > University Park, PA 16802 > 814 865-4752 > 814 863-6699 FAX > anton(a)bx.psu.edu > http://www.bx.psu.edu/~anton > http://g2.bx.psu.edu > > > On Jul 13, 2006, at 10:27 AM, Ross Hardison wrote: > >> The intersection tool under "Operate on Genomic Intervals (bx)" is >> not working for returning either overlapping regions or >> overlapping pieces. The intersection and overlaps in the non-bx >> operations section are working. >> >> I was running intersection (bx) on a set of Mathieu Blanchette's >> PReMods (118,402 regions) with our RP>0.05 intervals (314,040 >> regions), in hg17, requiring at least 10bp overlap. Here are the >> error messages. >> >> For returning overlapping pieces: >> An error occurred running this job: Traceback (most recent call >> last): File "./tools/new_operations/gops_intersect.py", line 63, >> in ? main() File "./tools/new_operations/gops_intersect.py", line >> 56, in main for line in intersect([g1,g2], pieces=pieces, >> mincols=mincols): File " >> >> For returning overlapping regions: >> An error occurred running this job: Traceback (most recent call >> last): File "./tools/new_operations/gops_intersect.py", line 63, >> in ? main() File "./tools/new_operations/gops_intersect.py", line >> 56, in main for line in intersect([g1,g2], pieces=pieces, >> mincols=mincols): File " >> >> I'll leave the files and results in my history for a while in case >> that is helpful. >> >> Thanks, >> Ross >> >> Ross Hardison >> T. Ming Chu Professor of Biochemistry and Molecular Biology >> The Pennsylvania State University >> 304 Wartik Laboratory >> University Park, PA 16802 >> e-mail: rch8(a)psu.edu >> phone: 814-863-0113 FAX: 814-863-7024 >> >> >> >> >> >> _______________________________________________ >> Galaxy-user mailing list >> Galaxy-user(a)bx.psu.edu >> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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PS on problem with intersection (bx)
by Ross Hardison 13 Jul '06

13 Jul '06

I forgot to tell you that I'm using the test version of Galaxy (http://test.g2.bx.psu.edu/) - Ross Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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