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3031 discussions

Re: [Galaxy-user] New version of Galaxy
by Julien Lagarde 23 Mar '06

23 Mar '06

Hi Anton, amazingly i was just about to send you the 'user account' suggestion ;-) does that mean that when sharing a history with other people, the history owner would be able to set basic read/write access to it? that would be very useful! i have another suggestion: when creating a new history item with the left-pane tools, and then editing its attributes to make it more human-readable, would it be possible to keep its original attributes somewhere? for instance: 1- i subtract gencode exons from my est alignments 2- i rename the output to 'ESTs not overlapping gencode exons' 3- i do whatever operation on 'ESTs not overlapping gencode exons'. let's say it gives me weird results, so i want to check if i did the right thing at step 1. AFAIK this is impossible right now. see what i mean? cheers j Anton Nekrutenko wrote: > Folks, > > A new version (2.2) of Galaxy is available at > > http://g2.bx.psu.edu:8889 > > Aside from completely new underpinnings it now features USER ACCOUNTS > and the ability to have MULTIPLE HISTORIES for each user. > > IMPORTANT -> THIS IS A TEST SITE. Once we move it to the production > level all histories will be LOST. > > The stable version of Galaxy, Galaxy2ENCODE and the old test site are > still available at the following URLs: > > http://main.g2.bx.psu.edu > http://encode.g2.bx.psu.edu > http://test.g2.bx.psu.edu > > SEND FEEDBACK to galaxy-user(a)bx.psu.edu > > ---------------------------------------------------------------------------------- > > New to Galaxy? See these two movies: > > Here is a short QuickTime movie showing Galaxy's usage example: > > http://www.bx.psu.edu/~james/galaxy_screencasts/JoinSNPs.mov > > A more complex example [requiring popcorn (or beer) -> 20 min] with > ENCODE data is here: > > http://www.bx.psu.edu/trac/local/encodeAnalysisExample.mov > ---------------------------------------------------------------------------------- > > > Thanks for your support! > > Galaxy Team > > > 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 > > > -- ---------------------------------------------- Julien Lagarde Genome Bioinformatics Research Group GRIB/IMIM Pg. Maritim de la Barceloneta 37-49 E-08003 BARCELONA - Spain Tel: +34 93 224 0886 --------------------

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Suggestion for galaxy
by anton＠bx.psu.edu 16 Mar '06

16 Mar '06

---------------------------- Original Message ---------------------------- Subject: suggestion for galaxy From: "Julien Lagarde" <jlagarde(a)imim.es> Date: Wed, March 15, 2006 6:56 am To: "Anton Nekrutenko" <anton(a)bx.psu.edu> Cc: "France Denoeud" <fdenoeud(a)imim.es> -------------------------------------------------------------------------- Hi Anton, here's an important feature galaxy should have, in our opinion: a 'restore deleted item' capability. E.g. the 'delete' link available for each history item should be a 'send to trash' instead. The user's trash should be easily accessible from the interface , 'empty-able' by the user, and emptied by your server e.g. every 2 days or so. thank you! j -- ---------------------------------------------- Julien Lagarde Genome Bioinformatics Research Group GRIB/IMIM Pg. Maritim de la Barceloneta 37-49 E-08003 BARCELONA - Spain Tel: +34 93 224 0886 --------------------

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[Fwd: Re: Randomization etc.]
by anton＠bx.psu.edu 15 Mar '06

15 Mar '06

---------------------------- Original Message ---------------------------- Subject: Re: Randomization etc. From: "France Denoeud" <fdenoeud(a)imim.es> Date: Wed, March 15, 2006 6:08 am To: "Anton Nekrutenko" <anton(a)bx.psu.edu> Cc: "Dan Blankenberg" <djb396(a)psu.edu> -------------------------------------------------------------------------- Anton, I used the randomozation tool, it seems to do exactly what I need it to do (and is faster than my script!) : thanks! Just two details: - the links to the UCSC browser are not working because of the "." in the 5th column (probably my mistake, as I put "." in the input file, because I am more used to gff format). - would it be possible to ask for several runs at the same time ? I usually generate 10 (sometimes 100) random sets to calculate the random overlap in a more robust way. Then, it would be usefull to be able to save the outputs all at once: is it possible in Galaxy? Two more general comments about galaxy: - would it be difficult to make it handle gff format? - would it be difficult to make it handle ENCODE coordinates (and add a tool to do the encode2chr conversion if needed ?). France. > France, > > Try new randomizer at http://test.g2.bx.psu.edu written by Dan > Blankenberg (djb396(a)bx.psu.edu) > > It is slower, but takes strands into account and returns correct > coordinates now. However, it not well tested yet, so be a beta-tester. > > 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 Mar 14, 2006, at 1:28 PM, France Denoeud wrote: > >> >>> France, >>> >>> We can change the tool to take care of the strand information. We >>> are currently re-writing our set operation and we'll redo the >>> randomizations as well (it uses the same underlying library). >>> This will take a few weeks. >>> >>> >>>> More worrying, they do seem to fall inside ENCODE regions (I looked >>>> using the "display at UCSC" link). >>>> >>> >>> This is normal as the tool currently only allows you to generate >>> regions within ENCODE. Do you want the whole genome? >>> >>> >>> >> Oops, >> I forgot a "not" : they do NOT fall inside ENCODE regions but at the >> beginning of the chromosomes, like if a shifting step had been >> forgotten... >> >>>> Another thing: I am trying to generate a random set mimicking a >>>> set of >>>> 616 objects and I get only 612 objects, is it normal ? >>>> >>> >>> You have 4 regions with length 1 (not really ranges, but points): >>> >>> chr7 116096515 116096516 racefrag_15 . + 1.0 >>> chr7 115906408 115906409 racefrag_13 . + 1.0 >>> chr19 60020799 60020800 racefrag_312 . - 1.0 >>> chr11 64079672 64079673 racefrag_561 . + 1.0 >>> >>> >>>> (by the way, is it possible in galaxy to be using two different >>>> "histories" at the same time?) >>>> >>> >>> Yes: >>> >>> 1. Click "share history" and bookmark the link >>> 2. Click "You may also create a new history by clicking here" >>> 3. Get the first query in and click "share history" and bookmark >>> >>> Now you can simply switch between the two using bookmarks (use >>> browser tabs) >>> >>> 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 >>> >>> >>> >> > >

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Error with ENCODEdb
by Prachi Shah 04 Mar '06

04 Mar '06

ENCODEdb queries don't work well. Here's the error message generated: error, format: interval, database: hg16 Info: 'module' object has no attribute 'BASEURL' Thanks, Prachi

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galaxy
by Laura Elnitski 03 Mar '06

03 Mar '06

Can galaxy put header lines between samples when returning genomic DNA? Other servers want to see the separation of sequences in FASTA files. 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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error erased history?
by Ross Hardison 26 Feb '06

26 Feb '06

The error that just occurred appears to have erased my history - is there any way to recover the history? - 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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error at Galaxy
by Ross Hardison 26 Feb '06

26 Feb '06

This occurred while getting phastOdds scores: exceptions.ValueError at /history I/O operation on closed file Python /usr/lib/python2.4/cgi.py in __getattr__, line 541 Web GET http://test.g2.bx.psu.edu/history Traceback (innermost first) /usr/lib/python2.4/cgi.py in __getattr__ self.file.seek(0) ... ▶ Local vars /usr/lib/python2.4/cgi.py in __repr__ return "FieldStorage(%r, %r, %r)" % ( ... ▶ Local vars /var/opt/universe/trunk-test/modules/Cheetah/Filters.py in filter filtered = str(val) ... ▶ Local vars in respond ▶ Local vars /var/opt/universe/trunk-test/galaxy/interfaces/common.py in fill_template return str(template) ... ▶ Local vars /var/opt/universe/trunk-test/galaxy/interfaces/root.py in history return self.fill_template(template, history=history, mode=mode ) ... ▶ Local vars build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in main ▶ Local vars build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in run ▶ Local vars Response so far HEADERS Date: Sat, 25 Feb 2006 18:52:04 GMT Set-Cookie: [] Content-Length: Content-Type: text/html Server: CherryPy/2.1.1 BODY Request information INPUT No input data. COOKIES Variable Value universe Set-Cookie: universe=6488ab1b7e827b13fd5e85de2ef78ab7; session Set-Cookie: session=2e41ce0777a1fcf0a6a2f9019dbec55f95e37934; universe_prefs Set-Cookie: universe_prefs=three; universe_ui Set-Cookie: universe_ui=info66;

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[Genecats] what is an efficient way to combine data tracks? (fwd)
by Belinda M. Giardine 24 Feb '06

24 Feb '06

Does someone want to tell this person about the benefits of Galaxy? UCSC has already told him about featureBits. Belinda ---------- Forwarded message ---------- Date: Thu, 23 Feb 2006 17:54:49 -0800 From: Jing Zhu <jzhu(a)soe.ucsc.edu> To: genecats(a)soe.ucsc.edu Subject: [Genecats] what is an efficient way to combine data tracks? Hi everyone, I need some help on a browser-related frustration I have been performing intersections of data from more than two tables (combining repeatmasker, simple repeats and pseudogene tracks) by using the TABLE BROWSER. But each step of this process takes a very long time to finish, mostly displaying "loading ... " on web browser. Although I manage to finish it, I would prefer a faster method. Can anyone give me a pointer for an alternative approach? I am currently working on combining tracks of functional annotation (Affy's gene expression track, refseq, mRNA, ESTs, and RNAs) for the whole human genome. Thanks in advance. Jing _______________________________________________ Genecats maillist - Genecats(a)soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genecats

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error message
by Ross Hardison 21 Feb '06

21 Feb '06

While using Galaxy ( http://test.g2.bx.psu.edu/) , the following error message appeared: Application Error An unexpected error occurred in the Galaxy framework. The error has been logged. Show details? (for developers) exceptions.NameError at /tool_runner/index global name 'httptools' is not defined Python /var/opt/universe/trunk-test/galaxy/interfaces/tool_runner.py in index, line 24 Web GET http://test.g2.bx.psu.edu/tool_runner/index Traceback (innermost first) /var/opt/universe/trunk-test/galaxy/interfaces/tool_runner.py in index return httptools.redirect( "/static/welcome.html" ) ... ▶ Local vars build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in main ▶ Local vars build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in run ▶ Local vars Response so far HEADERS Date: Sat, 18 Feb 2006 12:07:10 GMT Set-Cookie: [] Content-Length: Content-Type: text/html Server: CherryPy/2.1.1 BODY Request information INPUT No input data. COOKIES Variable Value universe Set-Cookie: universe=6488ab1b7e827b13fd5e85de2ef78ab7; session Set-Cookie: session=bd876117f1d3062e5902bbdf9e98e8533bc230ce; universe_ui Set-Cookie: universe_ui=info1%3Ainfo2;

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Problem using tools in local installation
by Sigurjón Axel Guðjónsson 18 Feb '06

18 Feb '06

Hi Galaxy team, Thanks for developing great platform for interactive large-scale genome analysis. We installed local mirror of Galaxy on linux machine. This mirror works well in connecting and getting data. But many of the tools are not working. It seems to be looking for binary files i.e. file named "galaxyOps3". Were can we find source code for that tool or any other tools using compiled binary files. best regards, Sigurjon -------------------------- Sigurjon Axel Gudjonsson Data Analysis and Management deCode genetics, Inc sigurjon.gudjonsson(a)decode.is Tel: +354 570 1871

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