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
hould have 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
value, dbkey, name, path
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 previ
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://toolshe
ncies that are properly defined in the tool config file
within the 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 par
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,
a link 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 wrote:
>> Hi Greg,
>>
&g
to take advantage of newer features, we 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
> li
ry%20Files
For all 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
lable to any local Galaxy instance is defined in the
tool_sheds_conf.xml file in the Galaxy install directory. For your local shed,
you'll simply need to an entry like this:
http://gvk.bx.psu.edu:9009/"/>
>
> p
>
>
> Paul Agapow (paul-michael.aga...@hpa.
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster 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 &#
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 to make this kind of documentation
> more visible...
>
If you are installing a single repository that contains a file
bx.psu.edu/Tool%20Shed
The specific section describing the process for automatically installing tools
to your local Galaxy instance is
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
Greg Von Kuster
On Mar 21, 2012
x27;t 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 Kus
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
> To: Alejandra Rougon
> Cc: Jennifer Jackson ; "
gt;
> > Thank you Greg, I saw the wiki but I do not see the admin link in my
> > galaxy interface. How do you open galaxy as an administrator?
> > t
> >
> > *From:* Greg Von Kuster
> > *To:* Alejandra Rougon
>
or all of the information 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 time
/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
You my need to install 3rd party dependencies for some tools.
Greg Von Kuster
On Feb 23, 2012, at 6:45 AM, Peter Cock wrote:
> On Thu, Feb 23, 2012 at 11:33 AM, Noa Sher wrote:
>> Hi
>
om smaller to larger 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 Kus
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"
in a good state. Thanks very much for reporting this issue.
Greg Von Kuster
On Jan 17, 2012, at 8:43 PM, Florent Angly wrote:
> Hi,
>
> I just tried to upload a new version of the Grinder Galaxy wrapper to the
> Galaxy ToolShed and am encountering difficulties that I did have in pre
brary%20Files
For details about Galaxy Data Libraries in general, see our wiki here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
Greg Von Kuster
On Jan 16, 2012, at 6:32 PM, Joshua Gross wrote:
> Hello all--
>
> We have set up a local version of Galaxy on our own server
e, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.
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 Lad
es on the left pane 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
>> file
The following provides specific details about the various options for uploading
files to data libraries.
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Let us know if you encounter any issues.
Greg Von Kuster
On Oct 27, 2011, at 4:31 PM, Oren Livne wrote:
> D
> mail.
>
> Thanks Anthony
>
>
>
> On 24/10/2011 19:01, "Greg Von Kuster" wrote:
>
>> I'm not following you here - please decipher your folder names, which I
>> assume are mapped to your encoded request strings.
>>
>> On Oc
is message or
> any part of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before opening or
> saving. HTTP://www.HPA.org.uk
> **
Greg Von Kuste
eremy, can you answer this one?
>
> Thanks again
>
> Anthony
>
>
> On 24/10/2011 14:09, "Greg Von Kuster" wrote:
>
>> Hello Anthony,
>>
>> On Oct 24, 2011, at 6:55 AM, Anthony Underwood wrote:
>>
>>> Permissions and private
psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
The Galaxy U
has been desired 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
___
The Galaxy User list should be used fo
$reference_file.value
>> #end if
>> [...]
>> #if str($homopolymer_dist):
>>-homopolymer_dist $homopolymer_dist
>> #end if
>>
>> #set $output_dir = $__new_file_path__
>> -output_dir $output_dir
>>
>>
][-1] }
>> #else if $reference_file.specify == "uploaded":
>>-reference_file $reference_file.value
>> #end if
>> [...]
>> #if str($homopolymer_dist):
>> -homopolymer_dist $homopolymer_dist
>> #end if
>>
>&g
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
o use this approach at the current
time, but you can plan on this much more streamlined approach in the future.
Greg Von Kuster
On Aug 8, 2011, at 9:52 AM, Paul-Michael Agapow wrote:
> So, I'm trying to setup a smooth pathway for our users to import their
> NGS data into Galaxy.
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
>
&g
t, you can 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'
>
&g
nes?
File "galaxy_dist/lib/galaxy/tools/__init__.py", 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:
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 use
your new biomart tool wrapper 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 h
galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
The Galaxy User list shoul
https://bitbucket.org/galaxy/galaxy-central/
Greg Von Kuster
On Dec 30, 2010, at 12:28 PM, Jean-Baptiste Denis wrote:
> Hello everybody,
>
> i'm a sysadmin in charge of installing a Galaxy server. I'm a totally
> beginner regarding this software.
>
> I've installed Gala
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