.
Shaun
Greg Von Kuster
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: davide.citt...@ifom-ieo-campus.it
*/
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What version of Galaxy are you running. I believe this issue was corrected a
while back, so can you update to the latest version?
On Feb 21, 2011, at 10:41 AM, Davide Cittaro wrote:
Hi Greg
On Feb 21, 2011, at 4:36 PM, Greg Von Kuster wrote:
Hi Davide,
Yes, in the Library actions popup
Galaxy lists, please use the
interface at:
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better reflected the intent. Let me
know if you disagree.
Thanks for your message!
Greg Von Kuster
On Mar 10, 2011, at 11:15 AM, Peter Cock wrote:
Hi all,
I've had a little play with our local Galaxy to try and get a feel for
libraries,
groups and roles.
I see when you create a new role
Hello Ry4an,
Thanks for the patch - it's been applied in change set 5214:0b9bba943c8f.
Greg Von Kuster
On Mar 10, 2011, at 6:15 PM, Ry4an Brase wrote:
Intermittently, and always during periods of high load we'll get a 500
Server error from the Admin 'Manage Jobs' list. In the logs
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Hello Peter,
Thanks for the patch - I've applied a corrected version of it in change set
5215:74c4dd43485a. Let me know if you'd rather have me flip the Copy data
into Galaxy? feature. I'd be happy to, but I don't want to reinvent the wheel
if you're close.
Thanks!
Greg Von Kuster
Hi Peter,
This has been resolved in change set 5217:70d7d0bfaad6, where I've changed the
check box into a select list per your suggestion.
Thanks!
Greg Von Kuster
On Mar 10, 2011, at 12:24 PM, Peter Cock wrote:
Hi all,
Via the Galaxy admin interface, I'm currently importing some BAM
, please use the interface at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
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Thanks
On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote:
Hello Greg
Thank you for answering. Please find the answers after each question.
Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit :
Hello Louise,
I do not think
-0400, Greg Von Kuster a écrit :
I assume when you dropped the old database and recreated the new,
empty database, you made sure the database connection string in
universe_wsgi.ini was correctly set. if so, when you started up
Galaxy, it would have created all of the required tables in the new
to our using LDAP?
Thanks
L-A
On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kuster g...@bx.psu.edu
wrote:
On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:
Here is the result I got from the debug statements:
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286
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will load two to three
times quicker. See our news brief at
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08
for details.
Perhaps you've discovered a different problem, but upgrading will at least
eliminate some known issues.
Greg Von Kuster
On Apr 15, 2011
, and for taking the time to
contribute your tools to the Galaxy community.
Greg Von Kuster
On Apr 18, 2011, at 3:58 PM, Vipin TS wrote:
On Apr 18, 2011, at 11:28 AM, Vipin TS wrote:
Dear Galaxy team,
I would like to upload a set of converter programs available for Generic
Feature Format (GFF
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Here is the problem, you must have something configured incorrectly in your
apache server that is not properly handling the request.
serving Galaxy through Apache
On Apr 29, 2011, at 9:10 AM, Greg Von Kuster wrote:
Hi Joachim,
Your hg environment looks good, so there must be something
Hello Leandro,
Try $input1.value_label
Greg Von Kuster
On Apr 28, 2011, at 10:17 AM, Leandro Hermida wrote:
Hi,
For a tool select input parameter:
param name=input1 type=select
option value=hs33Homo sapiens/option
option value=mm19Mus musculus/option
option value
Hello Louise,
Sorry about the delay, but significant time has passed since you sent the
message below, so I wanted to check with you to confirm this is still an issue
for you. Can you let me know?
Thanks,
Greg Von Kuster
On Mar 23, 2011, at 12:09 PM, Louise-Amélie Schmitt wrote:
Hi
that should eliminate datasets
falling into this category - not tested at all though...
On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote:
But I still have a question: It comprises the datasets stored in libraries
right? Is there a way to ignore them?
Greg Von Kuster wrote:
Hello Louise
list with the sum of
the file size of every dataset in each user's histories that don't belong to
any ibrary.
Is there a way to do that?
On Mon, May 16, 2011 at 7:18 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Louise,
I've pasted a diff below for the file ~/lib/galaxy/web/controller
://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
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it occur
with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting
whatever version of galaxy-dist was available about a week
and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini,
then your cached
that will help.
We are running whatever version of galaxy-dist was available about a week
and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Dave,
If you do not have a template_cache_path config setting
Lisa,
Thanks very much for reporting this bug. It has been fixed in our development
repo in change set 5608, which should be available in the distribution within
the next few weeks.
Greg Von Kuster
On May 31, 2011, at 8:39 AM, Liisa Koski wrote:
Hello,
I noticed a change in the newest
Greg Von Kuster
Galaxy Development Team
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/wiki/Home.
Greg Von Kuster
On Jun 7, 2011, at 6:21 PM, Joe Cruz wrote:
For my sample forms I have fields for Sample type, concentration, run type,
and read length.
I greatly appreciate your help Greg. If you have any other questions let me
know.
Thanks,
Joe
On Tue, Jun 7, 2011
to keep up on some of this documentation,
so hopefully we'll have something soon.
Greg Von Kuster
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to fill out all the fields repetitively.
joe
On Thu, Jun 9, 2011 at 3:20 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Joe,
Sorry you've bumped into problems - we know we're lacking on documentation
for the sample tracking stuff currently. I believe this new issue is due to
a field
Hi Peter,
On Jun 16, 2011, at 10:10 AM, Peter Cock wrote:
On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Peter,
I've added comments to each of these issues in bitbucket, and have pated
them inline below as well.
On Jun 16, 2011, at 5:03 AM, Peter Cock wrote:
Hi
it, create two samples (Sample1 and
Sample10) and assign the rest of the values to the corresponding fields for
each sample.
Thanks,
joe
On Thu, Jun 9, 2011 at 8:50 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Joe,
Try editing your Sample Form Definition, changing the Field name value
the tools get
updated?
---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, June 17, 2011 3:24 PM
if you bump into additional questions.
Greg Von Kuster
On Jun 22, 2011, at 5:41 PM, Shantanu Pavgi wrote:
Hi,
I have setup 'user_library_import_dir' to allow non-admin users to import
data libraries. The configured directory contains subdirectories with
galaxy-login (email) name. I
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AS f SET f.fields='%s' WHERE id=%i %(
fields_json, form_definition_id )
Greg Von Kuster
On Jun 28, 2011, at 6:58 AM, michael burrell (TSL) wrote:
Good Afternoon,
Firstly am a massive fan of galaxy, really like the things that it can do,
but I am a bit stuck updating our instance here
SET fields='%s' WHERE id=%i %( to_json_string( fields_list ), form_definition_id )
db_session.execute( cmd )
On Jun 30, 2011, at 12:04 PM, Greg Von Kuster wrote:
Hell all,
Michael discovered a bug in the
lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
, a new feature which I am currently implementing. It
should be available fairly soon.
Cheers,
Marcel
On 06/28/2011 10:05 PM, Greg Von Kuster wrote:
Hello Marcel,
Thanks for your message - see my inline comments below.
On Jun 28, 2011, at 5:55 AM, Marcel Schumann wrote:
Hi Greg
Hello Assaf,
Thanks very much for your patch - I've applied it in change set
5770:a5e0a5d3c0a1.
Greg Von Kuster
On Jul 1, 2011, at 5:35 PM, Assaf Gordon wrote:
Hi,
I'm trying to use the built-in cleanup scripts (instead of my own), came
across a possible bug:
1. When running
looks much better this way and the new metadata features
will certainly be very helpful as well ...
Cheers,
Marcel
On 06/30/2011 07:55 PM, Greg Von Kuster wrote:
This issue has been fixed - thanks for pointing it out.
Yes, attributes like tool_id, version, etc, fall
Hello Sarah,
This is a bug which I've fixed in change set 5776:a787213d08e1, which is
currently available from our development repository and should be available in
the distribution within the next few weeks. Thanks for finding this.
Greg Von Kuster
On Jul 8, 2011, at 3:53 AM, Sarah Diehl
Shaun, I forgot to mention, if you want to just fool around with tool shed
features, check out the test version of the tool shed at
http://testtoolshed.g2.bx.psu.edu/
On Jul 12, 2011, at 10:24 AM, Greg Von Kuster wrote:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi
You can now manage your repository's category associations in the tool shed.
On Jul 12, 2011, at 12:54 PM, SHAUN WEBB wrote:
I am, but I would like to be able to change the category. It will be an
RNA-seq tool.
Shaun
Greg Von Kuster
Galaxy Development Team
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.
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select to pull options (gtf annotation types) from
this file.
So I would somehow have to reference the file using the first parameter
rather than giving a hard-coded path.
Is that possible?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 09:23:19 -0400:
Hello Shaun
Hello Assaf,
Thanks for this patch as well. I've added it in change set 5792:a3fc507f2b42.
Greg Von Kuster
On Jul 13, 2011, at 1:53 PM, Assaf Gordon wrote:
Hi Greg (again),
This patch adds messages for the purge histories step:
1. A message is printed when processing a new history (so
Hello Ed,
Looking at the logs, I see that you uploaded to your Roche454 tool suite repo.
Is that correct? I don't see any exceptions in the logs, so not sure what
happened. Are you still having this issue?
Thanks,
Greg Von Kuster
On Jul 14, 2011, at 9:32 PM, Edward Kirton wrote:
Server
on a Mac. I've added exception
handling in the latest version of the tool shed that uses a different approach
to committing the changes whenever the intermittent exception is thrown.
Thanks for finding this issue, and please let me know if you bump into any
problems in the future.
Greg Von Kuster
Hello Christoph,
This is the result of a bug that I've corrected in change set
5819:0f15591f2acd, which should be available in our main Galaxy instance, as
well as the distribution, within the next few weeks. Thanks for pointing this
out, and very sorry for the inconvenience.
Greg Von Kuster
Hello Assaf,
I've added this to the ~/contrib directory in change set 5820:c609c2574c66.
Thanks very much for contributing this.
Greg Von Kuster
On Jul 19, 2011, at 2:45 PM, Assaf Gordon wrote:
Hi all,
I got around to writing the report I always needed: how much time each job
actually
Samuel,
Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py
for most of it. You should be able to find everything you need from there.
Greg Von Kuster
On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:
Quick question to you devs,
I need to find the code where
at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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working to resolve this
problem.
Your choice for organizing the files looks good.
Thanks for sharing your tool on the tool shed, and let us know if you come
across any other issues.
Greg Von Kuster
On Jul 22, 2011, at 11:37 AM, Lance Parsons wrote:
I recently created a new repository
, 2011 3:26 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Jelle,
There are a few things you need to do to add support for a new data type.
The steps are described here:
http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes
Greg Von Kuster
On Jul 22, 2011, at 8:49 AM
at it, feel free!
Thanks very much for your contributions!
Greg Von Kuster
On Jul 25, 2011, at 11:23 AM, Jelle Scholtalbers wrote:
Hi Greg,
this was indeed causing the problem. I added some code which now allows to
sniff image files. It is practically untested (it does work for me on bmp
Hi Peter,
On Jul 27, 2011, at 9:34 AM, Peter Cock wrote:
On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Helo Jelle,
I've taken a look at your patches and the code looks good.
However, I'm wondering why you find it necessary to upload image files to
Galaxy. Do tools
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.
Thanks very much for your contribution!
Greg Von Kuster
On Jul 25, 2011, at 11:23 AM, Jelle Scholtalbers wrote:
Hi Greg,
this was indeed causing the problem. I added some code which now allows to
sniff image files. It is practically untested (it does work for me on bmp,
jpg, png, tiff
it sooner.
Greg Von Kuster
On Jul 27, 2011, at 2:08 PM, Glen Beane wrote:
I should preface this by saying we are running a galaxy-dist that is a couple
months old now (we are planning on updating soon), but here is an annoying
issue we are seeing managing data library permissions:
The Roles
in the RequestsGrid class in
~/lib/galaxy/web/controllers/requests_common.py.
Good luck, and thanks for using Galaxy,
Greg Von Kuster
Sequencing Requests
Create new request
Advanced Search
NameDescription Samples TypeLast Updated ↑ State
No Items
For 0 selected items:
Submitted
, please use the interface at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
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Hello Sashi,
Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools
You probably want to base your tool config file on
~/tools/data-source/ucsc_tablebrowser.xml.
Greg Von kuster
On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote:
hi,
I have application , i want to integrate
Shashi,
You may find this wiki useful as well - sorry I missed it in my initial
response.
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote:
Hello Shashi,
On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote:
i have an application
Hello Steve,
Thanks for making this available. If you could email me the script, I'll
include it in the ~/contrib directory in the Galaxy distribution.
Greg Von Kuster
On Sep 2, 2011, at 3:20 AM, Steve Taylor wrote:
Hi,
We have written a tool that we call gls (galaxy ls). Running
at:
http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
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Hello Alex,
This issue was the result of a configuration error that should now be
corrected. Please let us know if you encounter further issues.
thanks for reporting this,
Greg Von Kuster
On Sep 9, 2011, at 12:41 PM, Alex R Bigelow wrote:
Hi,
I am a new developer interested in writing
, and local Galaxy instances will
install them from the Galaxy tool shed. This same process will be used for
populating our main Galaxy instance here at Penn State with tools. So for now,
please upload your tool to the tool shed.
Thanks again,
Greg Von Kuster
On Sep 9, 2011, at 4:08 PM, Dongjun
name like shed_tool_conf.xml, you should not
have a problem installing from a tool shed. I'll have a fix for the bug you've
discovered shortly, but making this change will fix the behavior until then.
Let me know if you bump into any additional problems.
Thanks for finding this!
Greg Von Kuster
://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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Tel: 858-736-3584
E-mail: jdu...@illumina.com
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Wednesday, October 05, 2011 6:25 PM
To: Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Tool shed and datatypes
Hello John,
The Galaxy tool shed currently
To clarify a bit more, there are currently only 2 languages supported in the Galaxy distribution; English and Japanese (note the 'en' and 'ja' subdirectories in the 'locale' directory). Setting your preferred language in your browser to Japanese will only render some Galaxy content in Japanese.
$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 written in preparation for it.
The new distribution will be available fairly soon
://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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%20Library%20Files
for all of the details.
Greg Von Kuster
On Oct 11, 2011, at 6:45 AM, alessandro albiero wrote:
Dear all,
I have a problem with galaxy and I have already tried to write on ther user
list
My problem concern the upload on galaxy of new files.
We are setting up a galaxy
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Galaxy Development Team
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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
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Thanks everyone for all the input on this!
Greg Von Kuster
On Oct 7, 2011, at 2:05 PM, Jim Johnson wrote:
Greg,
It would be great if there were a way to expand upon the core datatypes using
the ToolShed.
Would it be possible to have a separate datatype repository within the
ToolShed
:///galaxy_dbt?user=postgrespassword=postgres
This is all you need to do. Then start up the Galaxy server with:
sh run.sh
and Galaxy will automatically create all of the necessary tables for you.
Greg Von Kuster
On Oct 20, 2011, at 7:44 PM, Luciano Cosme wrote:
Hi,
I am sorry about the trivial
Von Kuster
Galaxy Development Team
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Of Chorny, Ilya
Sent: Friday, October 21, 2011 8:40 AM
To: Greg Von Kuster
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
files to my tool wrapper?
I need the base_url and the proxy. That is why I am using cookie_path. Any
: requirement type=datatypegmapdb/requirement
snpindex.xml: requirement type=datatypegmap_snps/requirement
snpindex.xml: requirement type=datatypesnps.iit/requirement
Thanks,
JJ
On 10/18/11 10:18 AM, Greg Von Kuster wrote:
Jim,
Sounds great - this will be very helpful!
Greg
Hello David,
I'm not sure why you're seeing this - do you mind if I try to delete all of the
files in your repository whose name ends in '~'? That may help me track down
the problem.
Greg Von Kuster
On Oct 26, 2011, at 3:09 PM, David Murphy wrote:
Hi
I've been trying to create
encounter further
problems. Sorry for the inconvenience with this.
Greg Von Kuster
On Oct 27, 2011, at 9:52 AM, David Murphy wrote:
Just realized I didn't reply to all, so the list didn't see this.
No problem at all, it would be much appreciated in fact.
Is there anything I need to do to do
day files in any way when it loads
them into a data library (e.g., prepend them with some metadata header), or
does it leave them intact and stores the metadata separately?
Thanks,
Oren
On 10/28/2011 1:44 PM, Greg Von Kuster wrote:
Hello Oren,
We use a sort of informal approach
on the list by using reply all
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Greg Von Kuster
Galaxy Development Team
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Please keep
along these lines?
Thanks again,
-J
On Mon, Nov 7, 2011 at 11:41 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello James,
This is not currently possible - the options for uploading files to Galaxy
data libraries is documented in our wiki at
http://wiki.g2.bx.psu.edu/Admin/Data
well.
Changes to be pulled:
3b384a62d359 by hanfeisun: Add locale files for Chinese
--
This is an issue notification from bitbucket.org.
You are receiving this either because you are the participating
in a pull request, or you are following it.
Greg Von Kuster
Galaxy
to and from external tools, etc all assumes the data is
sitting in a file, correct?
Thanks again,
-J
On Mon, Nov 7, 2011 at 6:29 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi James,
Since genomic data files are often very large, Galaxy does not store them in
a database, so this specific
, at 8:13 PM, Jim Johnson wrote:
Here it is.
JJ
On 11/9/11 5:14 PM, Greg Von Kuster wrote:
Hi Jim,
Would you mind attaching a tarball of the changed files you were attempting
to upload or push and send them to me? It would help me figure out the
problem.
Thanks!
Greg
On Nov 9
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Galaxy Development Team
g...@bx.psu.edu
for defuse. Thanks for discovering
this problem, and sorry for any inconvenience this may have caused.
Greg Von Kuster
On Nov 9, 2011, at 10:14 PM, Jim Johnson wrote:
Greg,
I had been trying to push from my local clone, as I had before. That failed
with a 404 error.
I next tried uploading
).
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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This issue has been corrected in change set 6261:26da65326612. The config
setting allow_user_deletion in universe_wsgi.ini must be set to true for the
operation buttons to be rendered.
On Nov 10, 2011, at 5:07 PM, Greg Von Kuster wrote:
On Nov 10, 2011, at 4:48 PM, Nate Coraor wrote
. If you
want it now you can pull from the central repo to get it.
Thanks for letting me know about this issue.
Greg Von Kuster
On Nov 22, 2011, at 10:22 AM, Sajoscha Sauer wrote:
Hi all,
We are just about to enable the Toolshed on our development installation of
Galaxy.
We run
Hello Sajoscha,
If you're pulling from central to get this fix, this is the change set that
should be used - it includes some additional fixes:
255f4bde822b
Again, sorry for the inconvenience.
On Nov 22, 2011, at 5:18 PM, Greg Von Kuster wrote:
Hello Sajoscha,
I've committed a fix
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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