Hi,
base:
os:centos6.4
torque:4.2.7
I built a glaxy cluster today,and then I found the job completion status of
torque queue is 'c',but the need state of galalxy is "ok".So I modified the
torque.py file and solved this error. I do, right?
diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/t
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data'
> 'Upload file from your computer'? Or the new upload dialog by clicking on
'Load Data'? Could you also please let me know if this error occurs always
or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014
it started to show us some weird behavior. Recently the upload function
suddenly stopped working properly. We are getting messages like the
following. I'm not sure if this only happens to us. If someone has seen
thi
Hi,
I'm having trouble with some of my tools not appearing in the Analyze Data
menu. I've successfully installed the tools via the manage installed tool shed
repositories(so they are installed to disk). I have tried uninstalling and
installing again. The tool installs but does not appear in
Hi Carrie,
The easiest solution at this point may be to generate diffs (e.g. with
`hg diff`) of the changes you want, and then apply those in clean
commits.
--nate
On Thu, Feb 27, 2014 at 10:10 AM, Ganote, Carrie L wrote:
> Hi Nate,
>
> Thanks for the reply! To answer/clarify your points:
>
>>.
Hi,
I just solved the problem.
1. The first Authorization problem was indeed in Apache. So, you have to define
the domain name. If there is a problem
Satisfy Any
Order deny,allow
Deny from all
Allow from your_ip
2. The second “403 forbidden” problem is actually allo
I'd add it here - https://wiki.galaxyproject.org/Admin/GetGalaxy
or perhaps here -
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, February 27, 2014 11:38 AM
To: Shrum, Do
Hi Donny,
it should be mentioned in the Tool Shed wiki, for example here:
https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
If you think the wiki is not sufficient, please add it to the wiki.
Where do you think that information is needed and missing?
Cheers,
Bjoern
Am 27.02.2014
I'm new to galaxy and I discovered during the install process...
That I needed a folder named ../shed_tools that is writable by galaxy.
migrated_tools_conf.xml:
shed_tool_conf.xml:
I spend a good chuck of time as a new user figuring this out so it's probably
worth adding to the docs if it's no
On Thu, Feb 27, 2014 at 4:20 PM, do kadya wrote:
>
> I don't think so that problem is in tool, because when I run same tool of
> normal terminal, it generate output.
This is why I was asking about Perl environment variables - they may be
different compared to when you run the tool. For example, i
Yes, that worked,
Thanks,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: al...@kucukural.com
Begin forwarded message:
> From: Hans-Rudolf Hotz
> Subject: Re: [galaxy-dev]
Hi Nate,
Thanks for the reply! To answer/clarify your points:
>.hgignore should not affect files that you have explicitly tracked (e.g. with
>`hg add job_conf.xml`)
I have a suspicion that when I tried to add a directory using Eclipse, I might
have added the whole repository, taking it all out o
Hi Carrie,
.hgignore should not affect files that you have explicitly tracked (e.g.
with `hg add job_conf.xml`) - if the file is tracked, Mercurial will
attempt to update and patch the working copy if there are upstream changes.
Also, it looks like your current tip includes neither .hgignore or
jo
I think you are right, and I am right, but you more so :). I bet the
inputs need to be dumped to json if files are being attached (i.e.
upload is being used) but should not be otherwise (because
content-type will be different). I wrote the client just to test
uploads - so this is probably the probl
Dear Developpers,
I'm still trying to use the bioblend function run_tool and now that I've
uptdated my version of galaxy, the problem comes from the input_dict
used to define the inputs. The command line generated is right except
for the inputs information, it is either None are sometimes, not
On Thu, Feb 27, 2014 at 9:32 AM, do kadya wrote:
> Hi,
> Thank You for your kind reply.
>
> I am having problem in running command in Galaxy.
> my current command:
>
>
>
>
> /usr/bin/x_tool fileList.tab file1.bam file2.bam
>
> I have created xml file so that i can run this command thr
Hi Alper
Have a look at ~/galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
check the line starting with
"main http://genome.ucsc.edu/cgi-bin/hgTracks?";
and add mm10
do a restart and you should get the link to 'UCSC main' for data mapped
to mm10
if that fixes the problem for
Hi all,
In a local instance of Galaxy, I rename all outputs of my users and
redirect their in a directory named with their usermail galaxy and then in
a directory named with the history.id.
To help them to retrieve their datasets, I want to display the
history.idat the top of the History left panel
Hi Nate,
without a trailing slash it works. I created PR #339, that removes
trailing slashes from tool IDs.
Thanks!
Bjoern
Hi Björn,
Please try it without the trailing slash on the tool ID.
--nate
On Wed, Feb 26, 2014 at 11:28 AM, Björn Grüning
wrote:
Hi Nate,
sorry to bother you aga
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