Dear
I am receiving the same error over and over again
WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with
extension 'coverage', using datatype from
/mnt/galaxyData/tmp/tmpuTitVp.
Whether I run
- Fastqc: Fastqc QC
You don't need a full PBS server on that machine, just the client libraries and
configuration. i.e. if you can run 'qstat' from machine A and have it return
the queue on machine B, that should be all you need.
We asked the IT guys they did just that :) now qsub works fine from
machine A!
Thanks nate,
I just would like to share others informations :
* I have added a VirtualHost, proxy and a DocumentRoot
* Consequently, RewriteRule have been modified :
Remplace
RewriteRule ^ galaxy/ (. *) http://ip:port $ 1 [P]
by
RewriteRule ^ / (. *) http://ip:port/ $ 1 [P]
It should be
Hello Yves,
You have one or more entries in your datatypes_conf.xml file for a datatype
named coverage These should be eliminated from your datatypes.conf.xml file
because they are not valid datatypes (unless you have added proprietary
datatypes to your Galaxy instance with this extension).
On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
Cool! Seems like a perfectly fine start. I guess you could
grab the # of sequences from the dataset somehow (I'm
guessing that is set somehow upon import into Galaxy).
Yes, I should be able to get
Hi Tanguy,
You can set that at the very bottom of your universe_wsgi.ini file. I
did it myself with Torque to set a different behavior for a couple of
tools, it works fine. The related Wiki page is here:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster :)
Best,
L-A
Le 17/02/2012
Hi Tanguy,
L-A is correct in that you can set using the tool id different cluster
options for different tools. For example I submit different tools to
different queues:
default_cluster_job_runner = drmaa://-q all.q -V/
upload1 = drmaa://-q short.q -V/
tophat = drmaa://-q long.q -V/
cufflinks =
If they used a package install, I think the DRMAA libs for torque are normally
separate. For instance:
http://pkgs.org/download/torque-drmaa
If going from source, you can enable DRMAA compilation with --enable-drmaa; I
don't recall if that is on by default (I don't think it is).
chris
On
This was recently brought up in a related thread by Nate, the code is in a pull
request on bitbucket. Changing the subject to see if that rings any additional
bells…
Here's the original post by John Chilton and link to the fork:
Thanks a lot Chris, actually we found another place where we found rpms
for PBS Pro:
http://apps.man.poznan.pl/trac/pbs-drmaa
And it works now! :D
Have a great weekend,
L-A
Le 17/02/2012 17:07, Fields, Christopher J a écrit :
If they used a package install, I think the DRMAA libs for torque
So I stopped using Apache as a proxy web server and use Galaxy as the web
server directly. This time the status of the sample data transfer changed
to Complete. So I believe Apache needs configuration modifications for
this case, maybe Apache needs mod_dav module and other related modules?
Re: PBSPro RPMs, that's actually good to know, we will likely need use of that
here as well.
chris
On Feb 17, 2012, at 10:30 AM, Louise-Amélie Schmitt wrote:
Thanks a lot Chris, actually we found another place where we found rpms for
PBS Pro:
http://apps.man.poznan.pl/trac/pbs-drmaa
And
Hello Luobin,
Thanks for sending the additional information. It sounds as if you are
using the default version of:
tool-data/shared/ucsc/ucsc_build_sites.txt
Adding hg19 to main in this file will add the link to the datasets.
Hopefully this helps,
Best,
Jen
Galaxy team
On 2/17/12 1:58 PM,
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