Hi there,
we have a 32 core server but I realised that a lot of programs are only
using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat
to use all of the cores but couldn't find an thread/core option for Macs14,
Macs2 or PeakRanger. Does anyone know if these programs are
Hi I am trying to load the mm10 genome and indexes using the manage
local data admin feature.
The genome downloads ok and so do the liftOver chain files, however
the main controller and indexing jobs fail. They just display error,
is there any way I can find out more about what is
Hi Alexander,
There is a -t for PeakRanger to indicate the number of threads. I
don't think macs14 or macs2 can run on mutltiple cores - I am cc'ing
Tao Lui, the author of macs, who can confirm this.
Thanks,
Q
On Tue, Mar 26, 2013 at 6:15 AM, Alexander Kurze
alexander.ku...@gmail.com wrote:
Hi Gordon,
Thanks for your assistance and the recommendations. Freezing postgres
sounds like hell to me :-)
abrt was filling the root directory indeed. So disabled it.
I have done some exporting tests, and the behaviour is not consistent.
1. *size*: in general, it worked out for smaller
Thanks Dan!
I am not sure about the dataset redirecting places other than ucsc and
wormbase genome browser.
By now, this can be done through Trackster right? Then I will
probably disable the external redirecting.
any comments/suggestions.
thanks,
--/Vipin
Hi Vipin,
Thank you for reporting
Hello Jereme,
I am going to post your question over to the galaxy-...@bx.psu.edu
mailing list to give it better visibility to the development community.
This is also where you will want to post future questions about your
local install.
http://wiki.galaxyproject.org/MailingLists
For you
Hello Joachim,
Joachim Jacob | VIB | wrote, On 03/26/2013 10:01 AM:
abrt was filling the root directory indeed. So disabled it.
I have done some exporting tests, and the behaviour is not consistent.
1. *size*: in general, it worked out for smaller datasets, and usually
crashed on
Jorrit,
Just to eliminate one possible cause of this behavior, could you confirm
that your local Galaxy instance's universe_wsgi.ini file's
enable_tool_shed_check setting is uncommented and set to True, and the
hours_between_check is also uncommented and set to a value between 1 and 12?
Hey Dave,
Thanks against for your quick response!
I checked my universe_wsgi.ini file and can confirm that the
enabled_tool_shed_check was *commented*.
I've uncommented the settings and changed them to:
enable_tool_shed_check = True
hours_between_check = 1
Then I followed the steps outlined
Dear dev-team,
I am interested to implement the secure hashed password specifically
SHA-256 or greater to the galaxy users using publicly available python
module PBKDF2.
I have a piece of python code which will do the job but not quite sure how
I can integrate this to my local galaxy code
Jorrit,
First, allow me to clarify a point of naming:
It's not quite right to say tools in this situation, as tools are only
one of several utilities that a tool shed repository can contain, along
with datatypes, workflows, repository dependencies, and so on. This is
an important
Thanks a lot for your answers. I tried to set the -t value to 32 in
peakranger but nothing really happens...it still runs on 1 thread even so
it says -t 32 in the execution line I guess I need to contact the author.
Thanks for your help!
Alex
On Tue, Mar 26, 2013 at 2:01 PM, Peter Cock
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