On 03/19/2012 10:19 PM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnsonmjohn...@ncbi.nlm.nih.gov wrote:
I'm writing some tools to integrate NCBI data resources with Galaxy. I have
two questions.
The first is simple. I want to write a tool for a long-running process that
is
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not
working in Galaxy has us making tool forms in ways we really don't
want to,
no one needs to use refresh_on_change or am I the only one that finds
it's broken? We've started to look at what Galaxy is trying to do,
On 3/19/12 5:19 PM, Peter Cock wrote:
Why do you need to do anything special at all for Galaxy here? I'd
just write it as a single command line call which blocks. As far as
Galaxy will know it is just a slow tool.
I suppose the tool could just poll the server, and only produce results
when
Hi Thon,
Thanks for reporting this. I see what the problem is here at least for the
clone duplication, and I've committed a fix in 6833:e8e361707865 that will
affect all workflows going forward.
Unfortunately, there isn't a complete solution for fixing the extra tags. The
problem was that
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster
(GridEngine). It's also running behind an Apache proxy now.
But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found
the documentation on this topic a
Leandro,
refresh_on_change is used quite a bit throughout the tool UI and appears to
work fine both on a local instance and on the public instance. E.g. look at
Tophat and change settings from 'Use Defaults' to 'Full Parameter List' -- the
refresh_on_change works on reload the tool with more
Hi David,
I don't know if you are still having this problem or not, but I did a
web search and found this thread on seqanswers from 2/16 that seems like
a good match to the problem you were having:
http://seqanswers.com/forums/showthread.php?p=65085
These scientists resolved the problem by
Hello all,
We are pleased to announce that early
registrationhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Registerfor the
2012
Galaxy Community Conference
(GCC2012)http://wiki.g2.bx.psu.edu/Events/GCC2012is now open.
GCC2012 will be held July 25-27, at the UIC
Forum
Dear Galaxy Developers,
This post went unanswered could I re-submit in a hope if there is any guy out
there who could stop me pulling my few left hairs.
My tool meant to load up (in a dropdown) some custom data from a non-galaxy
database for the user to select and submit a job. I am using
Hello Galaxy team,
I've recently begun building a resource usage monitor / predictor for
Galaxy as part of my Computer Science Honours degree and I was wanting to
at some later stage in my project, once the actual resource monitor is
built, to incorporate it to the actual Galaxy web interface.
Ed,
The top bar is defined in templates/webapps/galaxy/base_panels.mako. To create
a new masthead tab, you would have to edit that file in addition to creating
the relevant controller methods for the functionality you wish to add.
-Dannon
On Mar 20, 2012, at 8:32 PM, Edward Hills wrote:
I like this idea very much
but i think it might be better placed as a link in
http://galaxy.neb.com/admin
(maybe as a replacement for profile memory usage?)
brad
On Mar 20, 2012, at 8:53 PM, Dannon Baker wrote:
Ed,
The top bar is defined in templates/webapps/galaxy/base_panels.mako. To
Hello,
In the file lib/galaxy/tools/actions/__init__.py for the execute function
of the DefaultToolAction class line 198 has the following code:
if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey
in trans.user.preferences[ 'dbkeys' ] ):
In this case
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