August 2010 - galaxy-user - lists.galaxyproject.org

removing repeated entries from chip regions
by pande 26 Aug '10

26 Aug '10

Hi, Can galaxy help in removing the entries like this and convert these into one region like 149116122-149116142: chr1 149116122 149116141 region_27 0 + chr1 149116123 149116142 region_28 0 + chr1 149116124 149116141 region_29 0 + chr1 149116125 149116142 region_30 0 + chr1 149116126 149116142 region_31 0 + chr1 149116127 149116142 region_32 0 + thanks.

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integrating genomeview as display application
by Marijn Vandevoorde 25 Aug '10

25 Aug '10

Hi all, I'm trying to integrate genomeview as a display application. The configuration of the display applications seems to be pretty straightforward, but genomeview needs multiple input files. I can of course write a cgi file that will take a bunch of get parameters and use these as input files for the java applet. so on the side of genomeview, there's not really a big problem. however, to integrate it with galaxy, i don't see how to send multiple datasets to genomeview. you can only add the "view with genomeview" link to one dataset (or to all, but all will be viewed seperately). so i came up with the idea of a new datatype, .gvl, the genomeview list. in it, basically, a list of links to the datasets, so galaxy can work with them. i could make a tool, gvl creator, to take several datasets as input and then create a really simple textfile containing one url per line, for each dataset. i think this is the way to go (if anyone has better suggestions, please tell!) but now come the real questions: most important: how do i get the public url of my datasets? all other tools use the filesystem path, can't really find an example. and secondly: any idea how i could maybe take a dynamic number of inputs? i suppose that's not possible. this is not that big a problem. i could combine multiple gvl creators and then a gvl merger or something, no biggie! all help really appreciated. and of course i'll be happy to share everything with whoever is interested afterwards :-) with kind regards, marijn

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Galaxy Tool Shed now allows you to rate and review tools
by Greg Von Kuster 20 Aug '10

20 Aug '10

Hello Galaxy Community, The Galaxy Tool Shed at http://usegalaxy.org/community now allows you to rate and review tools contributed by others. Please keep sharing your tools - doing so provides a significant benefit to the community! Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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August 20, 2010 Galaxy Development News Brief
by Greg Von Kuster 20 Aug '10

20 Aug '10

The latest news brief is available at the following link. http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Problem in uploading the DATA
by asifullah khan 20 Aug '10

20 Aug '10

Dear Officer, I am a new user to assemble 75bp illumina solexa data. I have done single read illumina sequencing of my DNA of interest. it is a single file of about 370MB. The data, in file is initially in FASTQ format but letter the data arrangement become in some different kind of FASTq format inside the file. I want to convert the whole data in to simple FASTA format using GALAXY tools. I see the interesting videos on your site about using galaxy and it seems very interesting. But here i fail to upload my 370MB data file as an initial step. I am using 100Mbp LANE networking. Are you people preferring any other special network connection for uploading such huge files on GALAXY.? Kindly guide in this aspect. Moreover Kindly if possible then send me simple perl script and there command lines usage description for converting any format of FASTq in to FASTA. Regards, Asifullah Khan Research officer, DNA sequencing Labs, ICCBS, University of Karachi, Pakistan.

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Unable to run previously working workflows
by Manuel Leichsenring 20 Aug '10

20 Aug '10

Hello everybody, Since last evening (european time) I am not able to run any of my workflows successfully, even with data that previously worked. The results are rather inconsistent. Sometimes I get the message "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)", sometimes I get the message that the job was submitted successfully. I tried to turn on the the debug mode, but couldn't find the option. The workflow then is aborted at more or less random steps. Some parts of the workflow continue to the end sometimes, other times even the first step doesn't work, even if as simple as fetching flanking regions. A more frequent error is, that after joining two queries on genomic intervals, the result has wrong column annotations, i.e. after joining a 5-column query with a 18-column query the result only is said to have 5 columns (from the first file), although the data is added for all 23. I am posting this because I am not sure whether this is a current problem that is already being worked on, or whether I am the only one having it. Cheers Manuel -- GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 ¿/mtl.!* http://portal.gmx.net/de/go/dsl

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why is ./tools/sr_mapping/bowtie_color_wrapper.xml not implemented by default?
by Kevin Lam 20 Aug '10

20 Aug '10

Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml May I know if there's a reason for this? Cheers Kevin

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data upload via browser
by Nguyen, Doan 19 Aug '10

19 Aug '10

Regarding upload issue for large files that were recently populated, a possible resolution is to break your file into smaller chunks (chapters) and upload. You can then join or concatenate the files back. --------------------------------- Doan H. Nguyen, PhD Genetics and Gene Therapy Program Director, Microarray Core and Genome Bioinformatics Center 533 Bolivar St., Rm 539 CSRB New Orleans, LA 70112 Tel: (504) 568-4552 Lab: (504) 568-8001 Fax: (504) 568-8500 Email: dnguye(a)lsuhsc.edu ------------------------------------------

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galaxy over LAN
by TOLEN S 19 Aug '10

19 Aug '10

hi i want to use galaxy over my lan. i have install it on a Fedora 12 linux & even made changes to the host address in the universe_wsgi.ini to 0.0.0.0 but i access from other system in the lan. pliz help... thnx

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search in libraries
by Davide Cittaro 19 Aug '10

19 Aug '10

Hi all, how does the library search tool work? I'm trying on the public galaxy but I can't get any result... d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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