Hi everyone,
I am trying to modify the *recover* function from the drmaa.py
(/galaxy_central/lib/galaxy/job/runners/drmaa.py) as per my requirements.
But I am not ale to understand the flow of that function.
The recover function is called when the galaxy server is restarted. It first
looks for
Dear all,
I was thinking about how to improve some of my tools and
wondered if there is any way to have dynamic default values
for parameters (depending on other parameters).
Obviously this won't make sense in all cases, but as a specific
example, consider my Venn Diagram tool:
Harendra chawla wrote:
Hi everyone,
I am trying to modify the *recover* function from the drmaa.py
(/galaxy_central/lib/galaxy/job/runners/drmaa.py) as per my requirements.
But I am not ale to understand the flow of that function.
The recover function is called when the galaxy server is
Hi Peter,
Greg will probably reply, but I'll throw in my $0.02 as well.
Peter Cock wrote:
Hi Greg et al,
I've just been looking over your slides from last week about the new
'Galaxy Tool Shed', which are posted online here:
http://wiki.g2.bx.psu.edu/GCC2011
On Wed, Jun 1, 2011 at 3:22 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Peter,
Greg will probably reply, but I'll throw in my $0.02 as well.
Great - but with your answers you've triggered more questions ;)
Peter Cock wrote:
Hi Greg et al,
I've just been looking over your slides from last
Hello Peter - I finally got a chance to jump in - see my inline comments...
On Jun 1, 2011, at 11:00 AM, Peter Cock wrote:
On Wed, Jun 1, 2011 at 3:22 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Peter,
Greg will probably reply, but I'll throw in my $0.02 as well.
Great - but with your
Hi,
I have started galaxy daemon using 'reload' option. I am wondering if there is
a command to print currently used configuration values in the universe_wsgi.ini
file. It may help verify that configuration changes were reloaded.
--
Thanks,
Shantanu.
Hi Nate,
I got your point but which part of the code is doing all these things, I
mean how exactly this is done.
Is it using any other function apart from recover?
Regards
Harendra
On Wed, Jun 1, 2011 at 8:56 AM, Nate Coraor n...@bx.psu.edu wrote:
Harendra chawla wrote:
Hi everyone,
I
Harendra chawla wrote:
Hi Nate,
I got your point but which part of the code is doing all these things, I
mean how exactly this is done.
Is it using any other function apart from recover?
Yes, see __check_jobs_at_startup() in lib/galaxy/jobs/__init__.py
--nate
Regards
Harendra
On
On Wed, Jun 1, 2011 at 4:22 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter - I finally got a chance to jump in - see my inline comments...
Hi :)
What happens with branches? Would the Tool Shed just show the
default branch? That seems best for a simple UI.
Some of the branching
Peter Cock wrote:
Well, yes and no - as long as there are competing versions of a Galaxy tool
(e.g. from an original author and a fork by a second author), and they use
the same ID in their XML, you have a clash. This will have to be considered
in the (automated) install interface. i.e. In
John David Osborne wrote:
Hi,
We have run into a an error when trying to download a previously uploaded
file from our local galaxy instance (lives in a 512 MB VM). The error is at
the end of this message. In a previous thread, Nate advised setting use_debug
= False in universe_wsgi.ini.
Hi Nate,
Ya I have seen the function __check_jobs_at_startup(), it calls the recover
function after checking the state of the job from the database and updating
the jobWrapper. But what it does after calling the recover function and one
more thing, does it use the monitor() and the
On Wed, Jun 1, 2011 at 5:25 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
Well, yes and no - as long as there are competing versions of a Galaxy tool
(e.g. from an original author and a fork by a second author), and they use
the same ID in their XML, you have a clash. This will
Harendra chawla wrote:
Hi Nate,
Ya I have seen the function __check_jobs_at_startup(), it calls the recover
function after checking the state of the job from the database and updating
the jobWrapper. But what it does after calling the recover function and one
more thing, does it use the
(apologies in advance, limiting my response to the two questions below)
On Jun 1, 2011, at 11:54 AM, Peter Cock wrote:
On Wed, Jun 1, 2011 at 5:25 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
Well, yes and no - as long as there are competing versions of a Galaxy tool
(e.g. from
Peter Cock wrote:
If there is an official meta tool shed aggregator, that would address
my main concern about fragmenting things.
If nothing else, there can be a wiki page, although something
programatic would be more ideal.
... but we want to move away from the situation where someone
We use external authentication against our local LDAP directory - when
configured for external auth, Galaxy will automagically create a user
account the first time it sees a new user name from Apache - see
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
On Wed, Jun 1, 2011 at
It's also fixed in stable - the release right before the community
conference includes a bug fix for that fixes the URL generated for that
link.
--nate
Kanwei Li wrote:
Fixed on trunk by setting a default cntrller when there isn't one.
-K
On Thu, May 26, 2011 at 2:16 PM, Dave Walton
icho...@illumina.com wrote:
Have you made any additional progress on implimenting running DRMAA(sge)
jobs as different user (i.e. selecting which user)? Also, have you found a
way to integrate Linux usernames with Galaxy user names?
Hi Ilya,
This was a topic of much interest at the
Ryan Golhar wrote:
I just noticed a lot of files in my galaxy tmp directory. Since
this isn't a system tmp directory, the system cron scripts don't
clean it up.
Is there a galaxy cron script that can be used to clean up this directory?
Hi Ryan,
Sorry for the (very) late reply, I'm picking
Jean-Baptiste Denis wrote:
Hello everybody,
Hi Jean-Baptiste,
i'm in the process to provide Galaxy for multiple team. I've already
setup a testing instance using the production setup page on the wiki
(apache + sge) and it works quite well if i'm refearing to the users
feedback. This setup
On Wed, Jun 1, 2011 at 3:34 PM, Nate Coraor n...@bx.psu.edu wrote:
Jean-Baptiste Denis wrote:
My goal is to delagate the management of library/datasets to a galaxy
admin of each team from the beginning : i do NOT want a SINGLE
independant super admin to manage the access for multiple team, it
I looked at the Galaxy deployment presentation from the Galaxy Community
Conference (
http://wiki.g2.bx.psu.edu/GCC2011?action=AttachFiledo=viewtarget=GalaxyDeploymentandAPI.pdf
) and it was really helpful.
I am wondering if you could share any details or best practices for maintaing
the
I am wondering if galaxy tools directory structure can be changed so that tool
configurations resides outside galaxy code base. Right now the galaxy code
comes with some default/pre-installed tools in the $GALAXY_DIST/tools
directory. Any additional tool configurations are also defined in the
Louise-Amélie Schmitt wrote:
Hello everyone
I'm updating the remaining questions:
Hi Louise-Amélie,
I think it's possible that some of these were answered in person at the
community conference, but for a permanent record (and in case we
didn't actually answer them) here they are:
1) We use
Shantanu Pavgi wrote:
I am wondering if galaxy tools directory structure can be changed so that
tool configurations resides outside galaxy code base. Right now the galaxy
code comes with some default/pre-installed tools in the $GALAXY_DIST/tools
directory. Any additional tool
Hi Nate,
I was able to finally track down the login issue. It had to do with the
following setting in my universe_wsgi.ini:
*
*
*cookie_path = /galaxy*
Removing this out fixed the problem and I should be fine leaving it out out
since I don't need to run more than one instance of Galaxy. I
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