- galaxy-user - lists.galaxyproject.org

Finding Galaxy version
by Paul-Michael Agapow 19 Dec '11

19 Dec '11

A perhaps obvious question: how do I work out what version of Galaxy an instance is? This has come up a few times because of apparent bugs and different behaviour across various development and production instances. Now if you're installed straight from the repo, you can use "hg log" for the repo number. But that doesn't work if it's been installed in another way, say from a tarball or via another versioning system (we use git to synchronize tool development to a production server). Simple solution? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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comparing data sets with different coordinates
by dvera＠bio.fsu.edu 18 Dec '11

18 Dec '11

Hello, May I use galaxy to do correlation analyses with two continuous quantitative data sets containing different coordinates (two different microarray designs)? How can I create sliding windowed averages for these data sets to accomplish this? How can I perform a correlation analysis with a wiggle and a bed (e.g., microarray data VS gene density). Would I need to do a grouping of my microarray data with another spreadsheet defining the window coordinates? Thanks, Dan

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Performing operations on tab delimited text files
by Lanelle Oni Edwards 17 Dec '11

17 Dec '11

Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to my history. However, the first column of the data I imported is solely chromosome number and start and end position (ALL IN ONE COLUMN) in the format chrI:1000000-2000000. My question is: How can I filter out these values into separate columns using galaxy tools? For example: Having a separate column for chromosome number, column for start position, column for end position. I would really appreciate the help. Thanks, Lanelle Edwards Lab Manger University of Maryland

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(no subject)
by Giuseppe Petrosino 16 Dec '11

16 Dec '11

Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file". Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datasets (text manipulation) and then use MACS for the peaks calling? Thank you so much. Giuseppe

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about ftp setting up
by Liao_Ruiqi 16 Dec '11

16 Dec '11

Hello there， I'm a student at Fudan University in China. I was trying to enable ftp uploading in my local version of GALAXY. I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the following problems: 1. The galaxyftp seems to be a pasql database, shall I build it myself? or dose it already exists in galaxy directory? 2. the galaxy_user seems to be a table, shall I build it myself? and how shall I update it and integrate it with galaxy? Thanks for your attention, and looking forward to your reply! Best wishes Liao Ruiqi

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Extract genomic DNA
by Rebecca C Mueller 15 Dec '11

15 Dec '11

Hi all, Does anyone know if you can use the "Extract Genomic DNA" command with a genome not in the database? I am working with an algal genome (C. merolae) that isn't currently in the pulldown Database/Build menu. I keep getting the "Unspecified genome build" error, and am assuming that's the problem, as my other files appear to be formatted correctly (tab delimited without spaces for the intervals, same names for chromosomes in interval and fasta file, etc). Thanks! Rebecca

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Looking for Galaxy related papers (or have written one)? There is a new Galaxy Group @ CiteULike
by Dave Clements 15 Dec '11

15 Dec '11

Hello all, A new Galaxy Group <http://www.citeulike.org/group/16008/order/group_rating>has been created at the CiteULike <http://citeulike.org/> social bookmarking service to organize papers that are about, use, or reference Galaxy. The Galaxy Group<http://www.citeulike.org/group/16008/order/group_rating>is open to any CiteULike user (and anyone can become a CiteULike user). Group members can add papers to the group, assign tags, and rate papers. CiteULike makes extensive use of *tags* to organize and categorize papers. The Galaxy group uses this set of tags<http://wiki.g2.bx.psu.edu/CiteULike#CiteULike_Tags>to categorize papers. If you want to help other Galaxy users and sites find papers that are relevant to them, or help the Galaxy Project keep track of what papers (and communities) are using Gaalxy, then please help by adding relevant papers to the Galaxy Group Library<http://www.citeulike.org/group/16008/order/group_rating>and/or rating and tagging the papers that are there. *We particularly need help with papers that were published before this year, as very few of them are in the initial list. * Links: http:/galaxyproject.org/wiki/CiteULike - Explanation of tags http://www.citeulike.org/group/16008/order/group_rating - Galaxy Group list of papers Thanks, Dave Clements PS: To cite the Galaxy Project, see http://galaxyproject.org/wiki/Citing%20Galaxy. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Lastz very slow
by Andrew South 14 Dec '11

14 Dec '11

Hi - is there a reason Lastz is very slow right now? I am mapping 2-3,000, reads against a single, 11Kb, sequence and find that jobs are either returning an error or taking 16-24hrs to get done. This time frame was more like 30 minutes two weeks ago. Is there a way to speed this up? Thanks in advance for any help. Andy ************************************************************ Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096

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abolut ftp setup
by Richard Liao 14 Dec '11

14 Dec '11

Dear all, I'm a student at Fudan University in China. I was trying to enable ftp uploading in my local version of GALAXY. I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the following problems: 1. The galaxyftp seems to be a pasql database, shall I build it myself? or does it already exists in galaxy directory? 2. the galaxy_user seems to be a table, shall I build it myself? and how shall I update it and integrate it with galaxy? Thanks for your attention, and looking forward to your reply! Best wishes Liao Ruiqi

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GI error/shift in the output of megablast ?
by Sandrine Hughes 14 Dec '11

14 Dec '11

Dear all, I have a trouble with the Megablast program available in NGS Mapping and I hope that you can help. Indeed, I think that there might be a problem with the table given in output, and notably a shift between the GI numbers and the parameters associated. Here are the details: I. First, what I have done : I used the program to identify the species that I have in a mix of sequences by using the following options: Database nt 27-Jun-2011 Word size 16 Identity 90.0 Cutoff 0.001 Filter out low complexity regions Yes I run the analyses twice and obtained exactly the same results (I used the online version of Galaxy, not a local one). II. Second, I analysed the data obtained for one of my sequence (1-202). The following lines are the beginning of the table that I obtained after the megablast and two lines with troubles: 1-202 312182292 484 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 312182201 476 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 308228725 928 99.33 150 1 0 1 150 19 168 2e-75 289.0 1-202 308228711 938 99.33 150 1 0 1 150 22 171 2e-75 289.0 1-202 308197083 459 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392378 920 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392376 918 99.33 150 1 0 1 150 9 158 2e-75 289.0 1-202 300392375 922 99.33 150 1 0 1 150 11 160 2e-75 289.0 1-202 300392374 931 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392373 909 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392371 1172 99.33 150 1 0 1 150 9 158 2e-75 289.0 ... 1-202 179366399 151762 98.67 150 2 0 1 150 46880 47029 6e-73 281.0 1-202 58617849 511 98.67 150 2 0 1 150 21 170 6e-73 281.0 III. Third, what I’ve noticed: My first problem was that among all the species identified, two were very different from the expected ones (2 last lines). So I decided to search if that could be possible for this sequence and performed independently a megablast on the NCBI with similar options. I was not able to find these two species in the results. So, I decided to check the hits identified in the table above and identified a second problem. In the table, the second column give the GI of the database hit and the third column give the length of the database hit. However, when I manually checked in NCBI the length of the GI, this one was incorrect. Indeed, for the GI 312182292, the length should be 580 and not 484. By checking different lines, I noticed that the length that is given for a GI corresponds to the length of the GI-1. As you can see in the above table, some GI are consecutive (300392376, 300392375,...). When checking the length of 300392376 in NCBI, I should have 920. But when I checked 300392375, I found 918. And this was true for the following lines : 300392374 give normally 922 and 300392373 give 931... My conclusion at that point was that there is a shift of –1 between the GI and the other parameters of the line (indeed the parameters for the remaining columns are in agreement with the length of the GI-1). However, that’s not always true.... For some GI given in the table (for example, the two last lines), if we check the parameters of the GI-1, the parameters are completely different... So, I suppose that there is a problem in the GI sorting during the megablast but I’m not able to clearly define the problem. IV. Fourth, confirmed with an other dataset In order to be sure that the problem was not linked to my data or my process, I asked a colleague to do a megablast on independent data. The conclusions were similar to mine : a shift in the GI given in the table and the parameters associated on the same line, that most of the time but not always, correspond to GI-1. Can you confirm that there is a problem with the output of the megablast available in Galaxy ? If yes, do you think there is a way to fix it ? Thanks a lot, Sandrine

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