Hi,
I just noticed that this was another case of a tool that needs more then the 1GB memory that is
default on our cluster. After adjusting the job_runner settings everything seems fine.
regards, Andreas
On 15.11.2012 09:08, Andreas Kuntzagk wrote:
Hi,
when I start a lastz job it submits a
Hi,
I'm wandering how galaxy supports tools that are multithreaded or multi-process.
When working with lastz I noticed that it starts 4 parallel processes.
Is that always so? Can this be adjusted? What other tools also are
multi-process?
regards, Andreas
--
Andreas Kuntzagk
Andreas,
Yes this is possible. You can also have a look at the ncbi blast+ tools written
by Peter. The same is true.
Usually the tool wrappers (xml) have an option preconfigured how many threads
can be used... You can adjust these directly in the xml OR as we did we added
the option to be
Dear help;
How to get the human annotation file for RNAseq analysis, for mapping by BWA
and for RNAseq analysis, on Cufflinks and cuffdiff tools on galaxy?
Mira
Thanks
[image001]
Mira Bosso, M.Sc, B.D.S
Research associate
Pancreatic Islet Biology and Transplantation Unit
P.O.Box 1180,
You can use 'Get data' -- 'UCSC Main' to fetch an GTF (gene transfer
format) format of your species of interest, Human in this case. I tend
to use the Ensembl genes track (from the Genes and gene prediction tracks).
Make sure you use GTF as output, and send to Galaxy!
Cheers,
Joachim
Joachim
XGrid is a dead-end technology. It has been removed from OS X starting
with Mountain Lion (10.8).
--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153
On 11/22/12 9:47 PM, James Boocock smilefreak2...@gmail.com wrote:
Hi Galaxy Dev Team.
We are looking to put
Dear Galaxy help-centre
I want to use Tophat and Clifflinks to do an expression analysis. However, the
reference genome for Heterobasidion annosum (it is available at JGI) is not
listed. You have posted on your website that we can contact you if 'your
genome of interest' is not listed.
Is it
I was using Cufflinks to analyze Clip-Seq data. The results as 'gene
expression' and 'transcript expression' gave me almost same results (No. of
genes ? No. of transcripts). I guess the number of genes should be
relatively smaller than that in transcripts. I wonder if I need to get a
special
My account emailis so...@cc.umanitoba.ca
From: Songyan Liu [mailto:m...@cc.umanitoba.ca]
Sent: Friday, November 23, 2012 1:41 PM
To: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re. RNA-Seq
I was using Cufflinks to analyze Clip-Seq data. The results as 'gene
expression' and 'transcript
Can we also fetch virus file from some sources like this?
Thanks
Kanwar
On Mon, Nov 26, 2012 at 4:25 AM, Joachim Jacob joachim.ja...@vib.be wrote:
You can use 'Get data' -- 'UCSC Main' to fetch an GTF (gene transfer
format) format of your species of interest, Human in this case. I tend to
Hi,
Can you please send the entire link to access this changeset? I keep
searching for 5013377e0bf7 but can not find it.
Thanks in advance,
Liisa
From: Dannon Baker dannonba...@me.com
To: Sanjarbek Hudaiberdiev hudai...@icgeb.org
Cc: galaxy-...@bx.psu.edu
Date: 13/11/2012 12:34
Howdy, Andreas,
Lastz memory requirements are dependent on the size of the input
sequences (mainly on the size of reference sequence) and, to a lesser
extent, the genome's repeat content.
I'm a little confused/concerned by how this failure was indicated.
When run from a console, if
Howdy, Andreas,
The four processes started for a galaxy lastz job must involve post-
processing the lastz output through some other shell tool. Lastz by
itself doesn't support multiple threads or processes.
Bob H
On Nov 26, 2012, at 3:58 AM, Andreas Kuntzagk wrote:
Hi,
I'm wandering
Bitbucket will only show the first 7 characters when browsing through commits.
Try this:
https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7a656ea593098f1d1b38f3d6928c6
-Scott
- Original Message -
Hi,
Can you please send the entire link to access this changeset? I
Hi Joan,
For IGV and most external displays that work on BAM and other larger seekable
file formats (bigwig, bigbed, etc.) you'll need to use and configure a proxy
server for your local Galaxy instance that provides byte-range request
capabilities, such as nginx
On Nov 19, 2012, at 10:26 AM, Sajoscha Sauer wrote:
Hi,
We are running galaxy on the cluster with the 'real user' submission. It all
works fine, but at the end of the run we found something unexpected.
All the .dat files in the file_path folder are owned by the user running
Galaxy,
On Nov 19, 2012, at 12:49 PM, Harris Shapiro wrote:
Hello,
I'm writing because I've been trying for the past few days to configure
Galaxy to use Apache-based LDAP authentication, but have reached a point
where I'm basically stuck. The system in a virtual machine running:
- CentOS 5.8
Thanks Jeremy, Are there any resources linked with Galaxy for viral genome
seq annotation ?
I'm not aware of any viral genome annotations resources integrated into Galaxy,
but NCBI (and others) have virus gene annotations that you upload into Galaxy
and use.
Best,
J.
Hi,
I'm running IGVtools
(http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in
Galaxy on a WIG file but it's failing with exit code 1 and producing no
output file. On the other hand, IGVtools count and sort run successfully
in Galaxy on their respective inputs.
Also, IGVtools
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