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

galaxy 2.2 won't load
by Erika 30 Aug '06

30 Aug '06

Hi, I'm having 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, Tuesday August 29. The browser won't refresh or load the page. I tried using Safari 2.0.4 and internet explorer 5.2.3. However, the test site loads just fine. Thanks for your help with this! 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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sum of the length of regions
by Radek Szklarczyk 29 Aug '06

29 Aug '06

hi! i found it hard to get the sum of the length of regions. I ended up multiplying mean (sum stats) by the number of regions, for which I had to calculate the length with an expression first. Maybe I overlooked a simple way of getting what i want? radek --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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filter crash
by Radek Szklarczyk 29 Aug '06

29 Aug '06

Hi! I use galaxy 2.2 I extract all snps from snp125 (whole genome, hg17, i use ucsc browser main - UCSC: snp125 (genome) 2,771,857 regions, format: bed, database: hg17 ) and filter on expression: int(c3) - int(c2) == 1 I get an error: "An error occurred running this job: Code for line in file(inp_file): line = line.strip() if line and line[0] != '#': c1, c2, c3, c4, c5, c6 = line.split('\t') c1, c2, c3, c4, c5, c6 = str(c1), float(c2), float(c3), str(c4), float(c5), str(c6) if int(c3) - in" radek --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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Galaxy2.2 not accessible
by Ross Hardison 28 Aug '06

28 Aug '06

When I try to reach Galaxy2.2 (http://main.g2.bx.psu.edu/) it does not load, and I get the message: "Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /. Reason: Error reading from remote server" Galaxy2.2-Test does load and work OK. - 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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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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problem with gmaj
by Ross Hardison 25 Aug '06

25 Aug '06

I'm trying to use the GMAJ tool on Galaxy, but get this error: Error loading alignments from bundled file "input.maf": edu.psu.bx.gmaj.BadInputExceptions: Sequence length contradiction" s baboon.1 26891 63 + 1248010 TCAG... Current = 1248010. Previous = 550206 The maf files were extracted using the "Extract MAF blocks" tool, for TBA ENCODE alignments. The maf data are at http://main.g2.bx.psu.edu/display?id=3054

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broken link
by Cathy Riemer 04 Aug '06

04 Aug '06

>From the "WhatDoIDoFirst" wiki page: "In the second window open Galaxy by typing http://www.galaxy2.org in the location bar or by clicking below" Server not found Firefox can't find the server at www.galaxy2.org. -Cathy

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describe table schema
by Erika 03 Aug '06

03 Aug '06

Tools: Get data: UCSC Main table browser: when you click on "describe table schema" button, rather than getting the description of the table you get a message saying: "This is a proxy to the data services provided by the UCSC Genome Browser's Table Browser." any chance we can get the table descriptions? thanks, 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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Problems using GALAXY via the web server
by Jamil Bacha 02 Aug '06

02 Aug '06

Hi, I am trying to run some analyses using GALAXY but whatever I try keep getting a message returned saying /ERROR: [Errno 12] Cannot allocate memory/. My uploaded data files are in BED format with just the chromosome, start, end and name entered. I cannot find any obvious formatting problems with my files. Can you please advise. Many thanks Jamil

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help with maf file (upload?)
by Emmanuel Buschiazzo 01 Aug '06

01 Aug '06

Hi, I uploaded yesterday a .maf file (pretty big, ca. 55 MB). Despite a long waiting time, the upload did not seem to find an end (the webpage got stucked with the 'progression-display' full), and I had to close the window. However, the file now appears when I'm logged in. Despite this, when trying to use gmaj, no data seems to have the proper type. Also, when I try to 'display' my data file, there is a server error. Are these errors due to the file being corrupted because of the 'interrupted' upload? Is it something else? Thanks for your help. Emmanuel. <mailto:ebr26@student.canterbury.ac.nz>

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