Hello Joachim,
Thanks for reporting this. This issue was resolved a couple of weeks ago, but
did not make it into the cutoff for the last Galaxy distribution release. It
is corrected on the test Galaxy tool shed and will be included in the next
Galaxy release.
Greg Von Kuster
On Dec 12
been done automatically
for you when you installed the repository, but I'm not sure why it didn't.
Maybe you're running an older version of Galaxy that doesn't include this
automated feature.
Greg Von Kuster
!-- Locations of all bismark converted bs-seq references --
table name
available to your users.
Rolling back an installed tool shed repository within a Galaxy installation has
never been supported - instead just uninstall.
Greg Von Kuster
On Nov 14, 2012, at 11:06 AM, Paul-Michael Agapow wrote:
Just today, we had a case where we wanted to rollback to a previous version
Hello Joel,
The main Galaxy tool shed is back up - thanks for reporting this problem.
Greg Von Kuster
On Sep 30, 2012, at 5:34 PM, Joel Rosenberg wrote:
It looks like the galaxy toolshed is down.
The migration script is trying to download this:
http://toolshed.g2.bx.psu.edu/repository
Hello Fabien,
I don't understand the issue - can you provide a sample tool config that
includes these hard-coded paths? This initially sounds like an issue with the
tool configs, not the tool shed, but I may see the problem with your
clarification.
Thanks,
Greg Von Kuster
On Jul 3, 2012
that are properly defined in the tool config file
within the requirements tag set. These new tool shed features will soon be
documented in the tool shed wiki.
Thanks,
Greg Von Kuster
On Jul 3, 2012, at 12:27 PM, Fabien Mareuil wrote:
Hi,
Thank for your answer, I copy you a part of the shell
of the details about data libraries, see:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries
Greg Von Kuster
On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote:
We have large files that cannot be uploaded using the file upload command
and instead would need to be uploaded using a URL
can certainly do so.
Greg Von Kuster
On Apr 23, 2012, at 2:51 PM, Gregory Miles wrote:
Thank you very much for your help with this - we got that settled. One other
question...we are importing sorted, indexed bam files into a galaxy data
library and we are not having galaxy copy over
to the file (no copying). After at
least an hour of working, I get the error message Unable to finish
job,
tool error. Any thoughts as to how I can fix this? Thanks.
Greg
On 4/23/12, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Greg,
Even though you are not copying the data into Galaxy's
Von Kuster
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It may not be disclosed to any other person
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked
seen it yet -
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Library%20Security. Hopefully
it will clarify why you're seeing this. If not, you'll have to let me know the
permissions at all levels of your library in order for me to be able to help.
Thanks,
Greg Von Kuster
On Mar 10
as an administrator?
t
*From:* Greg Von Kuster g...@bx.psu.edu
*To:* Alejandra Rougon alerou...@yahoo.com
*Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
*Sent:* Tuesday, 28 February 2012, 14:02
*Subject
No, you'll need to stop and restart your Galaxy server.
On Mar 1, 2012, at 2:01 PM, Alejandra Rougon wrote:
I did close the web browser and opened it again
was that enough?
From: Greg Von Kuster g...@bx.psu.edu
To: Alejandra Rougon alerou...@yahoo.com
Cc: Jennifer Jackson j...@bx.psu.edu
on Galaxy data libraries, see this wiki:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
Greg Von Kuster
On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote:
Hello, I tried to search in the forums and although this question has
appeared many times I still don't have a solution.
I
numbers
(e.g., 89 - 90, 90 - 91, etc). Your migrate_versions.version database table
column has a value of 90, but your ~/lib/galaxy/model/migrate/versions
sub-directory has scripts only up to 0079... (or so it seems). Not sure how
best to fix the problem...
Greg Von Kuster
On Feb 21, 2012, at 2:21
David, I can answer your first question, but will leave it to others to answer
your second as I am less likely to answer it correctly.
Regarding uploading files from your server, use the Upload files (to data
libraries) from file system paths but do not copy into Galaxy's default file
store.
Hello Efthymios,In case no one on this list answers, you may be able to get an answer to your question by contacting the owner of the velvetoptimiser repository. You can do this by selecting the "Contact repository owner" menu item on the View repository page.On Dec 20, 2011, at 4:02 AM, Makis
the interface at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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in Analyze Data. How
can I access it and use its files in workflows?
Oren
On 10/27/2011 7:55 PM, Greg Von Kuster wrote:
Oren,
The best way to do this would be to use galaxy data libraries, uploading
files from file system paths and not copying the files into the Galaxy file
location
On 24/10/2011 19:01, Greg Von Kuster g...@bx.psu.edu wrote:
I'm not following you here - please decipher your folder names, which I
assume are mapped to your encoded request strings.
On Oct 24, 2011, at 1:27 PM, Anthony Underwood wrote:
Re: [galaxy-user] Permissions and private roles
Anthony
On 24/10/2011 14:09, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Anthony,
On Oct 24, 2011, at 6:55 AM, Anthony Underwood wrote:
Permissions and private roles
Hi all
I’m trying to get my head round permissions on Data Libraries. I have a
couple of questions
1) When I come
**
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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for some
time, but is not on our near-future plans for implementation.
Thank you,
Florent
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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Galaxy analysis and other
$base_name = $output.id
-base_name $base_name
;
$script2 $output_dir $base_name
/command
On 04/10/11 22:55, Greg Von Kuster wrote:
Hello Florent,
Sorry for the confusion on this - we are preparing a new Galaxy
distribution, and the tool shed wiki has been
Hello Louise-Amelie,
This behavior was corrected in change set 5612:3297ec86d657, which should be
available in the distribution within the next week or so. Sorry for the
inconvenience.
Greg Von Kuster
On Jun 20, 2011, at 11:06 AM, Louise-Amélie Schmitt wrote:
Hello everyone
, line 1867, in
_prepare_datasource_json_param_dict
rval[ key ] = self._prepare_datasource_json_list( val )
NameError: global name 'val' is not defined
Greg Von Kuster
On May 31, 2011, at 11:06 AM, Liisa Koski wrote:
I am also getting the same error with my local biomart and local galaxy
pull the fix from our development repo at
https://bitbucket.org/galaxy/galaxy-central.
Greg Von Kuster
On May 31, 2011, at 11:52 AM, Liisa Koski wrote:
Hi Greg,
I thought I was up to date. When I run the following command I get 'no
changes found'
hg incoming
real URL is https
in the script is 60. To remove
files from disk on the same day they were marked as deleted, override the
default by setting the -d flag to 0.
Greg Von Kuster
On Apr 30, 2011, at 4:59 PM, Simon Lank wrote:
Hi.
Our current galaxy database is ~ 600 gb, most of which are user deleted
datasets
to your tool_conf.xml file and start up
your Galaxy instance.
For details about adding a new tool, see
https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial.
Greg Von Kuster
On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:
Hello
I have looked at the biomart plugin for Galaxy
at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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