- galaxy-user - lists.galaxyproject.org

redundant datasets
by Ross Hardison 19 Apr '06

19 Apr '06

I wanted to repeat a request that when datasets of the same name are deposited on different dates, that only the more recent one be shown on the Galaxy menu. For instance, under ENCODE/Transcriptional Regulation, users can get either TR (20060204) or TR (20060206) The latter is the one they should use. Thanks, 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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slow loading home page
by Ross Hardison 19 Apr '06

19 Apr '06

Do you have any idea why it takes so long to load the homepage http://www.bx.psu.edu/cgi-bin/trac.cgi when you come from the Center home www.bx.psu.edu ? It used to be instant, but now it takes several seconds. Yesterday, I just stopped showing Galaxy to a visitor because the page did not load after what seemed like a long time (maybe 10-15 sec). - 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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Problem in set-up of "coverage" operation
by Ross Hardison 15 Apr '06

15 Apr '06

The "coverage" tool is a great addition to the set, but I think the description is backwards from the execution. The user selects: The density of elements of Query: (call it query 1) within Query: (call it query 2) The explanation says: "Return entire regions from query 1 that overlap query2, and append two more fields at the end of the returned region: (1) the number of nucleotides for each returned region from query 1 that overlap a region from query 2 and (2) the percentage of the overlap for each region of query1: ..." What you get is actually the opposite of the explanation. You get the regions from the 2nd query that contain regions from query 1, etc. The selection tools have query 2 as the target for finding elements from query 1, but the explanation treats query 1 as the target. I think the first choice should be query 1 and the second choice be query 2. You could change the explanation, but I think it would be better to change the selection display. In that case, you would have something like: Within Query: (pull down menu of choices for the target) Find the density of elements of Query: (pull down menu of choices for elements to find in the target). Then the explanation will fit. 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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2 bug reports
by Ross Hardison 14 Apr '06

14 Apr '06

I'm reporting two problems on the most recent Galaxy (lavender background, http://g2.bx.psu.edu:8889/) (The header says "logged in as jb10(a)sanger.ac.uk) 1. Problem running overlap: When I ran overlap on the transcriptional regulation composite hits (Transcription Regulation (TR (20060206) [gencode_partitioned])) and a CpG island track, I got the following error message: An error occurred running this job: ERROR: commandline error, substituting {'input2': './database/files/dataset_265.dat', 'input1': './database/files/dataset_282.dat', 'input2_strandCol': '0', 'min': 1, 'dbkey': u'hg17', 'input2_chromCol': '1', 'out_file1': './database/ files/dataset_283.dat', 'input2_startCol': '2 ', 'input2_endCol': '3'} into galaxyOps3 $dbkey -chromCol=$input1_chromCol -startCol= $input1_startCol -stopCol=$input1_endCol -strandCol=$input1_strandCol -chromCol2=$input2_chromCol -startCol2=$input2_startCol -stopCol2= $input2_endCol $input1 $input2 -all -chrom=all -minSize=$min -bed= $out_file1 -> 'input1_chromCol' Other tracks did overlap just fine. 2. Problem with "Select lines that match an expression" I got empty files back when I tried two different things. No error was reported, but the result reports " Select on data 30 empty, format: interval, database: hg17 Info: Illegal output filename. 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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proximity search
by rmorin＠bcgsc.ca 12 Apr '06

12 Apr '06

Hi there. I am trying to find the genes that are within 10kb (in the upstream region of the gene) of a set of genomic features. The proximity search works fine for this, but what I am really interested in the actual distance between the given feature and the gene. It appears all I am getting back is the list of genes from the query. Is it possible to use Galaxy to actually get these distances at this point? Thanks. Ryan

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Re: [Galaxy-user] galaxy problems
by Anton Nekrutenko 11 Apr '06

11 Apr '06

Dear Mark, Thank you very much for your e-mail. This is exactly the kind of feedback we are looking for to make Galaxy better serve your needs. We will take a hard look at these problems. Below a quick comment on gff: > (1) First of all, I try to load a gff file - that works fine. But > the "edit > attributes" won't correctly assign the columns to the data for doing > interval stuff - I try to do an overlap, and it says something about > startcol being undefined. Currently we treat gff at simple tab delimited file as this is the easiest way to deal with its o-1 incompatibility with bed format. To use bed in interval operations use GFF-to-BED converted (test.g2.bx.psu.edu -> Convert Formats)\ Thanks, 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 Apr 11, 2006, at 7:55 PM, Mark Bieda wrote: > Hello All, > I'm a member of the ENCODE TR group and have done a fair amount of > programming. > Galaxy seems a well-designed approach to analysis. > But there are a number of problems, it seems, in my basic testing. > (1) First of all, I try to load a gff file - that works fine. But > the "edit > attributes" won't correctly assign the columns to the data for doing > interval stuff - I try to do an overlap, and it says something about > startcol being undefined. > (2) Generally, I strongly advise that you allow direct loading of > gff data > and recognition of this format. It's easy to do. (But this is lower > priority, I understand). > (3) So I create my own interval files as a test - one file is a > subset of > the other, with a small difference in the sizes of some intervals > (with > strand information, FYI). I compute the overlap and the difference. > The > overlap is correct, the difference looks probably ok. I then do the > union > of the overlap and the difference. This should lead to my original > data - > but no, it doesn't. > (4) I mention the strand information because it seems that the > difference > eliminates this info (bizarrely) and the overlap keeps it. > (5) As a general comment, I would say that I am quite used to > bioinformatics and programming. If I am having these sorts of > problems, > this will be very hard on more experimentally oriented biologists. > > Ok, so I'm writing this because, like I said, Galaxy looks like a very > well-thought out approach to doing this stuff - I'm impressed with the > overall project approach - but I think that it doesn't seem to be > working > very well right now - or you are over my head. > > Say hello to Ross Hardison for me, and I look forward to hearing > from you - > > Also, I've attached files for your testing > Mark > > Mark Bieda, Ph.D. > UC-Davis Genome Center Postdoctoral Fellow > Farnham Lab > <largerset_hg17.txt> > <smallerset_hg17.txt> > _______________________________________________ > Galaxy-user mailing list > Galaxy-user(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

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Error running Galaxy on windows XP
by Ryan Morin 10 Apr '06

10 Apr '06

Hello developers. I have just installed Galaxy on my Windows XP machine to try it out. I am having a problem running the server locally. I ran the galaxy.py script with no errors and I can load the page it generates in my browser. However, when I attempt to load some data from the UCSC (following the flash demo) I am not able to load the UCSC table browser. When I run the test script (base_test.py) I get the following printout (see below). I'm sure it's something simple but I don't have the expertise to try to debug this. Can anyone help me out? Thanks. Ryan C:\galaxy\tests>c:\Python24\python base_test.py *** adding to sys.path Testing individual deletes ... ERROR Testing metadata editing ... ERROR Testing home page ... ERROR Checking data for multiple uploads ... ERROR Testing single upload ... ERROR ====================================================================== ERROR: Testing individual deletes ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\galaxy\tests\test_util.py", line 41, in setUp self.home() File "C:\galaxy\tests\test_util.py", line 50, in home tc.code(200) File "c:\galaxy\eggs\twill-0.8.3-py2.4.egg\twill\commands.py", line 115, in co de TwillAssertionError: code is 407 != 200 ====================================================================== ERROR: Testing metadata editing ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\galaxy\tests\test_util.py", line 41, in setUp self.home() File "C:\galaxy\tests\test_util.py", line 50, in home tc.code(200) File "c:\galaxy\eggs\twill-0.8.3-py2.4.egg\twill\commands.py", line 115, in co de TwillAssertionError: code is 407 != 200 ====================================================================== ERROR: Testing home page ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\galaxy\tests\test_util.py", line 41, in setUp self.home() File "C:\galaxy\tests\test_util.py", line 50, in home tc.code(200) File "c:\galaxy\eggs\twill-0.8.3-py2.4.egg\twill\commands.py", line 115, in co de TwillAssertionError: code is 407 != 200 ====================================================================== ERROR: Checking data for multiple uploads ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\galaxy\tests\test_util.py", line 41, in setUp self.home() File "C:\galaxy\tests\test_util.py", line 50, in home tc.code(200) File "c:\galaxy\eggs\twill-0.8.3-py2.4.egg\twill\commands.py", line 115, in co de TwillAssertionError: code is 407 != 200 ====================================================================== ERROR: Testing single upload ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\galaxy\tests\test_util.py", line 41, in setUp self.home() File "C:\galaxy\tests\test_util.py", line 50, in home tc.code(200) File "c:\galaxy\eggs\twill-0.8.3-py2.4.egg\twill\commands.py", line 115, in co de TwillAssertionError: code is 407 != 200 ---------------------------------------------------------------------- Ran 5 tests in 0.218s FAILED (errors=5)

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error message
by Laura Elnitski 05 Apr '06

05 Apr '06

Hi- I'm trying to filter the data from 3-way RP scores on the UCSC browser before importing into galaxy and I'm getting this error message from both the test browser and main browser: There has been a problem connecting to http://genome.ucsc.edu/cgi-bin/ hgTables? [Errno socket error] (-3, 'Temporary failure in name resolution') Thanks, Laura

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Chip-chip data
by Laura Elnitski 30 Mar '06

30 Mar '06

Hi- the chip-chip data is in wiggle format and galaxy sends this message error, format: wig, database: hg17 Info: ------------------------------------------------------------------------ --- Reached output limit of 100000 data values, please make region smaller, or set a higher output line limit with the filter settings. ------------------------------------------------------------------------ --- A search for only chr 7 produces the same error as the whole genome search. Is there any way to do a minimum of one chromosome at a time? Thanks very much, 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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test
by Anton Nekrutenko 24 Mar '06

24 Mar '06

test 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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