- galaxy-user - lists.galaxyproject.org

connection request
by Belinda M. Giardine 22 Jun '06

22 Jun '06

I just got an email from a user that was having some problems with the GALA - rVista connection. As GALA is not far from being retired it would be nice if Galaxy2 could step in and become the new link from rVista and Mulan. This would be a good connection for users working with binding sites. Thanks, Belinda

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please copy history to galaxy 2.2
by Julien Lagarde 15 Jun '06

15 Jun '06

Hi when are you planning to move to the new version? could you please save my history when you do? http://g2.bx.psu.edu:9000/share_history?id=17 thanks julien -- ---------------------------------------------- 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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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 16 May '06

16 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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