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

Downloading Galaxy I expect newer stuff than I get.
by Gunnar Þór Sigurðsson 31 May '06

31 May '06

Hi! I downloaded the Galaxy source with this command from you webpage: svn co http://coltrane.bx.psu.edu:8192/svn/universe/prototype/trunk galaxy_dist At the end of the checkout I get this message: "Checked out revision 1035." But when I start the server and get the webpage up, there it says: Galaxy Version: 2.1 Revision: $Rev: 720 $ I was hoping to get v2.2 and actually there are like 300 revisions difference between what it says I checked out and what starts up. Any ideas????? Regards GunS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Gunnar Thor Sigurdsson Phone +354 570 1979 Data Management deCODE genetics Sturlugata 8 gunnar(a)decode.is IS-101 Reykjavik www.decode.com Iceland - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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Test Server Updated
by Dan Blankenberg 30 May '06

30 May '06

This is just a quick note to let you know that version 2.2 has been pushed up to test.g2.bx.psu.edu. Your old data is not lost, but is available temporarily at g2.bx.psu.edu:8887. Please let me know of any errors encountered at test.g2.bx.psu.edu - depending on your browser, you may want to clear your cache. Thanks, Dan

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suggestion
by Kateryna Makova 22 May '06

22 May '06

Is it possible to have an option of displaying results in a separate window? This would be helpful for some of the things we are doing... Thanks, K. ************************** Kateryna Makova Assistant Professor Department of Biology Center for Comparative Genomics and Bioinformatics 518A Mueller Lab Penn State University University Park, PA 16802 E-mail: kdm16(a)psu.edu http://www.bx.psu.edu/makova_lab/ Tel: (814)863-1619 Fax: (814)865-9131

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extracting opossum sequences from UCSC Test browser
by Melissa Wilson 19 May '06

19 May '06

The opossum sequence is assembled into chromosomes in the UCSC test browser, but I am, thus far, unable to extract the nucleotide sequence that corresponds to a given chromosomal location. Previously when I went to "Get Data" at the most recent opossum assembly in the test browser it would act as if it were extracting the BED file, but there would be " # no results from query" and I could not extract the genomic sequence corresponding to my chromosomal location (chr7:32478949-32483556) in opossum. The query turned red and I received the following error message: "An error occurred running this job: <font color="yellow">BED fields are missing. Possibly no strand information is present</font>. I assume this is because no BED file was actually extracted from the table browser. Now, when I "Get Data" from the UCSC Test browser now I can't even get to the most recent opossum data in the UCSC test browser. When I try to switch from Human to Opossum I am sent to the "UCSC Table Browser" page with the statement, "This is a proxy to the data services provided by the UCSC Genome Browser's Table Browser" Is there a different way to extract the sequences corresponding to the current assembly of the opossum genome? Thank-you very much, Melissa

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SVN problem...
by Guillaume Bourque 18 May '06

18 May '06

Hi, I'm trying to install Galaxy locally. I'm getting the following error message: [macgbg5:~] guillaum% svn co http://coltrane.bx.psu.edu:8192/svn/universe/prototype/trunk galaxy_dist svn: PROPFIND request failed on '/svn/universe/prototype/trunk' svn: PROPFIND of '/svn/universe/prototype/trunk': could not connect to server (http://coltrane.bx.psu.edu:8192) Do you think it's a problem with the way I installed svn or it's a problem with the path? Thanks, Guillaume

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question on Galaxy function
by Yutao Fu 17 May '06

17 May '06

Hi, there I tried to use the "Compute PhastCon Score" function on the Galaxy web interfact and got this error message: "Interval must match exactly one target region". Could you help me to get through? The history link is : http://encode.g2.bx.psu.edu/share_history?id=7baccfa4198d1e95ec8ed91d911a46… The website is very useful and convenient. Thanks. Yutao __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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2.2 test problem on mac
by Hefferon, Timothy (NIH/NHGRI) [E] 12 May '06

12 May '06

Hi, I work on a mac, and find that the 2.2 test version of Galazy doesn't work (specifically, a server error in the right-most field where my search results should show up). Any reason 2.2 doesn't work, while the otehrs do? Thanks! Tim

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server error - help please
by Hefferon, Timothy (NIH/NHGRI) [E] 10 May '06

10 May '06

Hi, I am trying to use Galaxy to (1) obtain a multiple alignment file from the genome browser, and (2) convert it to multiple-FASTA format using the Galazy utility. I am getting an "Unrecoverable error in the server" error. I have attached the multiple alignment file that Galaxy gave me. Can you please help? Thanks, Tim

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running galaxy trunk release on localhost and serving it via proxy
by rmorin＠bcgsc.ca 07 May '06

07 May '06

Hello. I am currently running the latest version of galaxy on my web server at localhost:8080. I have the server set up to proxy to this port to allow access to galaxy (using the information posted here: www.cherrypy.org/wiki/BehindApache) I tried using both the rewriterule method and the proxypass method to no avail. I'm just wondering if you might have encountered this situation before. When I go to the URL that should proxy to galaxy, I get the title of the page ('galaxy') and error 404 (http://srna.mbb.sfu.ca/myrna) I have included the relevant portion of my httpd.conf file if you are interested. I would appreciate any advice you could give as you are all very experienced with the subtleties of CherryPy. Thanks. Ryan by the way, I am running the latest release of SuSE on this server. >From http.conf: ProxyRequests On <Proxy *> Order allow,deny Deny from none Allow from all </Proxy> #tried with this first, got the same result #RewriteEngine on #RewriteRule ^/myrna(.*) http://localhost:8000/$1 [P] <Location /myrna> Order Allow,Deny Deny from none Allow from all ProxyPass http://localhost:8000 ProxyPassReverse http://localhost:8000 RequestHeader set CP-Location /myapp </Location>

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error running galaxy on localhost
by rmorin＠bcgsc.ca 03 May '06

03 May '06

Hello. I am trying to set up a copy of Galaxy on my local SuSe Linux machine. I have it running on localhost. I get the following error message when trying to get the genomic sequences for a set of coordinates: "error, format: fasta,database: hg17 Info: Cannot open /depot/data1/cache/alignseq.loc No such file or directory" I'm guessing that the program assumes a certain directory structure to be in place (including a path called /depot/data1/cache). Just wondering if there are other directories I will need to create to get this system running smoothly. I could not find any documentation regarding this on the Galaxy setup page. If such documentation exists, I would be very appreciative if you could point me towards it. Regards. Ryan P.S. Great application nonetheless!

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