So here is what I've installed so far. (/usr/local/galaxy) is a
directory that all nodes in the cluster can see. And the web server
machine can also see it.)
$ls -l /usr/local/galaxy
drwxrwxr-- 20 galaxy scicomp 2206 Nov 8 15:53 galaxy-dist
-rwxrwxr-x 1 galaxy scicomp 1882 Nov 8 15:34
On Nov 7, 2012, at 5:47 AM, Diam Hsu wrote:
Dear Sir or Madam,
I used to use Galaxy to analyze NGS data, but these two days I could't login
my Galaxy account, it also told me that my account has been marked deleted,
and asked me to contact the Galaxy administrator to restore my
Hi Ross,
Thanks for the suggestions. I'm aware that this is not really a
Galaxy-specific question, and I've been browsing through SeqAnswers and
found a couple of suggestions using edgeR or DESeq, but nothing for Tuxedo
suite. However, I have no experience with either of these tools, so I was
Dannon,
Maybe you can, but not through me. I'm just a lowly user and
biologist. You would have to contact the guy who did the installation
and runs the server: Lei Yan (leiyan2...@gmail.com)
I would think he would be receptive to some help, so you should mail him.
LTR
On 11/7/12 4:05 PM,
It looks like both the main server and our local install are frozen.
Nothing has run since we started yesterday at about 11:30am. Anybody
know why?
LTR
On 11/7/12 4:05 PM, Dannon Baker wrote:
Main will complete the jobs eventually, though obviously that's not
particularly useful in the
Hi,
I am performing online tophat on 5 different samples which I want to compare
for gene expression. Is there any simple way, after the end of tophat for all
of them, with which I can have an excel table with the 5 samples and their hits?
Something similar to this
Vevis1
Vevis2
Vevis3
It isn't normal, but this can happen during periods of extremely high load like
we're currently experiencing. If you leave your jobs in the queue, they'll
execute as soon as possible - don't cancel or restart your jobs as this will
only move them to the back of the queue and delay completion.
Lei -
It looks like you have two worker nodes, but both are currently listed as
non-idle, yet have low load. My guess is that something has gone wrong with
the SGE configuration causing jobs to simply wait in the queue. If you look at
the contents of qconf and qstat on the admin page, does
Kristis,
This data is available further downstream in an RNA-seq analysis pipeline,
specifically, as output from the Cuffdiff tool. Take a look at the page for
more details:
https://main.g2.bx.psu.edu/rna-seq
Best,
J.
On Nov 9, 2012, at 3:42 AM, Vevis, Christis wrote:
Hi,
I am
I'll take a couple of stabs at this. First, make sure that /scratch/galaxy
exists.
There's an error at the bottom of your pastie that seems to indicate it's not
there.
Second, you're right about virtualenv not being used. It is likely that root
is being used, which means that all of the
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