Hi All,
I am a new user of Galaxy. I am trying to configure galaxy on my local
system. I took clone of repository(https://bitbucket.org/galaxy/galaxy-dist).
But I have couple of issues while understanding code base:
1. Is there any help file explaining directory structure and what all
Hi
1 - You might want to read the bitbucket wiki instead:
https://bitbucket.org/galaxy/galaxy-central/wiki/Home
There you can find all the information you will need to understand the
configuration files, but don't expect a detailed description of the
whole directory structure. The information
Does anyone have practical info on galaxy setup on a cluster?
Robert C. Jackson
Software Systems Specialist III
The University of Texas Pan-American
Computer Support Services
Division of Information Technology
Phone: 956-665-2455
Fax: 956-665-8777
Does anyone know how to get SRMA to work properly in galaxy? I've used the
pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the
result of an SRMA re-alignment job in both instances is a python process which
only takes a few percent CPU (or less, since it only seems to be
Hi there,
Looking at the output of the SplicingDiff files of CuffDiff, me and my
colleagues are preplexed about the output of the p_values and q_values.
We've tried different inputs of different samples to compare but never seem
to manage to get p_values smaller than 0.50 and we keep getting
Robert Jackson wrote:
Does anyone have practical info on galaxy setup on a cluster?
Hi Robert,
Please see the production server documentation at:
http://usegalaxy.org/production
--nate
Robert C. Jackson
Software Systems Specialist III
The University of Texas Pan-American
Computer
Hello Robert,
You may have a look at the official documentation on the wiki:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
You may also have a look at the slides from the past Galaxy Community
conference:
Felix,
You seem to be providing the correct inputs to Cuffdiff and it appears to be
producing valid output. More information about setting parameter values and
interpreting Cuffdiff can be found in manual:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Good luck,
J.
On Jun 16, 2011, at
What version of Cufflinks is your Galaxy installation running? A recent version
(1.00 and 1.01) had a problem that was causing the splicing and promoter use
tests to have very few differentially regulated genes, according to
http://cufflinks.cbcb.umd.edu/.
-rory
On Jun 16, 2011, at 8:13 AM,
I was wondering how to get a hold of the axt and/or nib files required by
alignseq.loc. It's not mentioned on the local NGA Galaxy setup page. I was
surprised to learn that: Fetch Sequences - Extract Genomic DNA requires
AXT or NIB alignment files in order to extract mouse genomic DNA from
Hi,
anyone tried to install an aspera server for a galaxy cloud instance? The goal
would be to feed some local data faster to the instance.
best,
joe
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The Galaxy User list should be used for the discussion of
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Hello,
I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed
illumina FASTQ data and used Bowtie to map it to hg18. I then used MACS to
call ChIP-Seq peaks; over 13,000 were identified. Analysis of individual
peaks shows good consistency with ENCODE data sets on UCSC, so I
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