It's in the [app:main] section. See the universe_wsgi.ini.sample file for the
exact position-- this file will always be up-to-date with the initial
configuration options that might have shown up as you've updated your galaxy
instance.
-Dannon
On Mar 22, 2012, at 7:50 PM, Jose Navas wrote:
>
Hi Dannon,
Thank you for your quick answer. I search in my Galaxy instance's
universe_wsgi.ini and I didn't find this option... Where can I add this option?
Thanks,
Jose
> Subject: Re: [galaxy-dev] HTML output with Javascript
> From: dannonba...@me.com
> Date: Thu, 22 Mar 2012 19:44:05 -0400
> C
Assuming everything is generated correctly for the html report, what you're
probably running into is Galaxy's html sanitization. In your Galaxy instance's
universe_wsgi.ini you can set the following option (to false) to disable this:
# Sanitize All HTML
# By default, all tool output served as '
Hi Galaxy developers,
I have a tool that generates an html output which executes some javascript
functions that are defined in a *.js file. I put this file under the
$output1.files_path but when I display the html file in the galaxy browser, it
doesn't executes the Javascript. What can I do to
Hi Jianpeng,
For reference, this is the wiki with instructions:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
The first thing to double check is that the server has been restarted.
This is necessary after adding new indexes.
The next check is to walk through the setup steps again and ma
The fellows here working on galaxy, about ready to release it to prime time,
came to me asking about a few sudo commands that they needed. looking into it I
came across a discussion
(http://osdir.com/ml/galaxy-development-source-control/2011-11/msg00067.html)
from last November talking about wh
Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File "./scripts/cleanup_dataset
Hi;
I'm getting an error when comparing two datasets (two tabular files)
with "Join, substract and group" (Error pasted bellow). If I execute
joinWrapper.py manually I don't get the error, and also it doesn't
happen if I use the Galaxy version changeset 5743:720455407d1c. Any
clues? Any help
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not
to be integrated in any other platform. I think that the idea is to use
galaxy as another user of your system.
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed
On Thu, Mar 22, 2012 at 3:34 PM, Daniel Sobral
wrote:
> Hello,
>
> For certain tools, like bwa or blast, there is a non-configurable number
> of threads to use inside the tool xml.
> This is inconvenient for certain cluster configurations, where what we
> want is division of a job into multiple jo
It's always best to look at examples in the code base for technical details
like this rather than the wiki. You probably will need a combination of a
constructor along with a select list item in your tooll There
are many tools that include these types of constructors that refresh the page
w
In the past, every time I ran into this issue, cleaning browser's
cookies fixed my problem.
On Thu, Mar 22, 2012 at 11:50 AM, Andreas Kuntzagk
wrote:
> Hi,
>
> For our fresh new local instance I created a user. But whenever I try to
> login it looks like I end up as anonymous user again. And if I
Hi,
For our fresh new local instance I created a user. But whenever I try to login it looks like I end
up as anonymous user again. And if I click "Workflows" I'm told that I need to login first.
The only thing that looks like an error message is this one:
"galaxy.web.framework DEBUG 2012-03-22
Dear Nate,
thanks! I got back to my installation and followed your advice, amending
my vhost.conf files and I can now, at least, import data from my private
UCSC browser into Galaxy.
I'll now look into your "next stable release" to get the other direction
running.
Cheers a lot!
Fred
On 1
Hello,
For certain tools, like bwa or blast, there is a non-configurable number
of threads to use inside the tool xml.
This is inconvenient for certain cluster configurations, where what we
want is division of a job into multiple jobs (I guess this is what is
intended by the tag), and not creatio
Hello,
I was wondering if there is a way to trigger the reload of a tool's
configuration from command line.
We are using a tool that loads .xml files from tool-data. The .xml files
get modified by a script ran by cron frequently. Right now we reload the
tool config via the admin interface but
I'm working on an data source tool for NCBI's
Sequence Read Archive (SRA). I'm currently targeting a small form
in the existing SRA application, to allow downloading a part of a
specific assembly. The form I'm talking about is labeled
"Alignment" on this page:
Andrew,
You are correct. I've made this change in galaxy-central changeset 4d48285fcaa6
Thanks,
J.
On Mar 20, 2012, at 9:18 PM, Andrew Warren wrote:
> Hello,
>
> In the file lib/galaxy/tools/actions/__init__.py for the execute function of
> the DefaultToolAction class line 198 has the follow
A good approach would be to perform a simple diff on the local version and the
.sample and make appropriate changes to the local version. You can also use
mercurial to view the changeset log per file, but this is probably not as
simple.
For example,
diff universe_wsgi.ini universe_wsgi.ini.sa
thanks for the clear update. But, how does the end user know which are the
files got updated by the incoming changeset, as I see many files get modified
by the update proces? I know "sanitize_all_html" is a new addition which I can
incorporate manually, but I don't know which are other addition
Hi leandro,
We're resurrecting the Galaxy sample tracking system, so you'll be seeing some
work coming from us in this area over the coming weeks. Support for the
components will also be more timely and efficient. As usual, contributions are
welcome!
On Mar 22, 2012, at 8:05 AM, Leandro Herm
Hi Daniel,
On 22 March 2012 08:20, Daniel Sobral wrote:
> Hello,
>
> At the moment I don't think there is a way to restrict usage of specific
> tool(s) to specific user(s).
> Is anyone thinking on developing this kind of functionality?
> I guess it might be a bit complicated to implement?
>
> I
Hi Raj,
The files associated with each .sample file (universe_wsgi.ini is associated
with universe_wsgi.ini.sample, datatypes_conf.xml is associated with
datatypes_conf.xml.sample, etc) are your local versions of each of these files,
allowing you to set configuration values according to your ow
Hello Dev team,
I normally use "hg incoming" to check for any updates and "hg pull -u" to
install new updates if available. I noticed that there are files created with
".sample" extension after the update (for all config files) - eg
"universe_wsgi.ini.sample" is modified with new updates, but
Thank you Tyler and Carlos it's working.
Siva
> From: carlos.borr...@gmail.com
> Date: Wed, 21 Mar 2012 16:26:48 -0400
> Subject: Re: [galaxy-dev] Change "Manage data Libraries"
> To: nsi...@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
>
> Yes. For example setting "library_import_dir =
> /GALA
Dear Greg,
On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster wrote:
> Leandro,
>
> For refresh_on_change to work you need a set of optional selections and a
> set of refresh_on_change values, so in your example, the type should
> probably be a select instead of data. You'll also need the select l
Hello,
At the moment I don't think there is a way to restrict usage of specific
tool(s) to specific user(s).
Is anyone thinking on developing this kind of functionality?
I guess it might be a bit complicated to implement?
I guess an "easier" alternative is to have different galaxy instances
runni
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