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
bjoern.gruen...@gmail.comwrote:
Hi
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
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
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,
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
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
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 of
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 h...@fmi.ch
Subject: Re:
On Thu, Feb 27, 2014 at 4:20 PM, do kadya doka...@gmail.com 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.
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:toolbox tool_path=../shed_tools
shed_tool_conf.xml:toolbox tool_path=../shed_tools
I spend a good chuck of time as a new user figuring
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'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,
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
Location /display_application
Satisfy Any
Order deny,allow
Deny from all
Allow from your_ip
/Location
2. The second
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 cgan...@iu.edu wrote:
Hi Nate,
Thanks for the reply! To answer/clarify your
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 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
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
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