Hi,
I updated to the latest galaxy distribution (after one year). And now
every job fails with:
/home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify
limit: Operation not permitted
The limit is ridiculously high:
ulimit -v 6000
Its just to prevent some badly
Hmm... this is probably a script that works fine on your login node
but not on your worker nodes or vise versa? The fact that it is
writing to standard error and happens for each new shell is probably
what is causing Galaxy jobs to fail - Galaxy is thinking the
underlying applications are writing
I have no issue with supporting this in general - but the
implementation I think is a bit more tricky than it would seem. The
test framework doesn't know if Galaxy would uncompress zipped files or
not - I think the only way to reason about that in the abstract is to
actually upload the file to
Hello,
I'm trying to analyse a 384-plate screen genome data set(67 plate size)with
DecoRNAi tool to discover the over represented seed family, and I got this
error:
An error occurred running this job: Error: cannot allocate vector of size 617.8
Mb.
Any idea of why? Is there a limit on the
Hello Lance,
I cannot think of a good way to rescue these jobs. If you are
curious about the code where jobs are selected for execution - I would
check out the job handler (lib/galaxy/jobs/handler.py) - see
__monitor_step for instance.
It seems like to prevent this from happening in the
Hello,
I've been spending a bit of time looking over Data Sources
https://wiki.galaxyproject.org/Admin/Internals/DataSources for Galaxy.
I've been thinking about designing a tool in Galaxy, similar to a Data
Sources tool, which would take as input a file defining a list of URLs to
import into
I had the brilliant idea of sending the previous email out on a Friday
afternoon/evening. I'm just following up with this thread.
Best regards,
Bruno
--
Bruno Grande, B.Sc. (Hons)
M.Sc. Candidate
Dr. Ryan Morin's Laboratory
Molecular Biology and Biochemistry, Simon Fraser University
did you check if the metadata on the input was set correctly/at all?
This happens sometimes in our galaxy instance. Metadata is not set correctly,
and jobs run after metadata is set by hand.
No reupload necessary.
best,
ido
On 06 Nov 2014, at 17:13, Lance Parsons lpars...@princeton.edu wrote:
