- galaxy-user - lists.galaxyproject.org

Data imports hang
by Ross Hardison 05 Sep '06

05 Sep '06

I encountered a new problem while going through a Galaxy example for my class, using Galaxy2.2. When importing data from the UCSC Main Table Browser, the history column does the usual count-down of "refreshing in 10 sec, 9 sec, 8 sec, ...", but once it stops at "refreshing in 1 sec". Then it just shows the spinning wheel indefinitely. Clicking on "refreshing in 1 sec" completes the import, and now you get the data in 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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no mm5 sequence data in galaxy 2.2
by Radek Szklarczyk 04 Sep '06

04 Sep '06

when i try to download sequences for mm5 (uploaded bed file) i get an error: 4: Extract genomic DNA on data 2 An error occurred running this job: <font color="yellow">No sequences are available for musMus5</font> For hg17 it works correctly. --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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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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