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 +
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:
how do i get the public url of my datasets? all other tools use the
filesystem path, can't really find an example.
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,
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
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
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
Moreover Kindly if possible then send me simple perl script and there
command lines usage description for converting any format of FASTq in to
DNA sequencing Labs,
ICCBS, University of Karachi, Pakistan.
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.
GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 ¿/mtl.!*
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.
May I know if there's a reason for this?
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
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.
how does the library search tool work? I'm trying on the public galaxy but I can't get any result...
Cogentech - Consortium for Genomic Technologies
via adamello, 16