I'm running a test Galaxy system on a cluster (merged galaxy-dist on
Janurary 4th). And I've noticed some odd behavior from the DRMAA job
runner.
I'm running a multithread system, one web server, one job_manager, and
three job_handlers. DRMAA is the default job runner (the command for
tophat2 is dr
I am trying to understand how FTP and data library upload options are working
in Galaxy. When a non-binary file is uploaded through FTP option, it goes
through three move operations:
1. First it is copied to a temporary namespace line-by-line converting newlines
2. Then the temporary file is m
Hello Joachim,
Tool dependencies are installed into the location defined by the following
entry in your universe_wsgi.ini file.
# Path to the directory in which managed tool dependencies are placed. To use
# the dependency system, see the documentation at:
# http://wiki.g2.bx.psu.edu/Admin/Conf
Hi Brad,
Sorry that didn't fix your issue and I agree that your traceback hasn't changed.
I've committed another potential fix in galaxy-central changeset
8542:530fb4f8204f, but it is hard to be certain that I have replicated your
exact issue. Could you try that changeset to see if that resolve
Hi all,
Updating our Galaxy: the migration of some tools to the toolshed (let's
take picard as an example) and installing them back from the toolshed
worked well.
However, during the update, I forgot to install the dependencies.
So I went to the administration part of our Galaxy, and selecte
Hi,
I installed Galaxy locally. I would like to check with you if its installation
package has everything necessary.
galaxy-galaxy-dist-36ad8aa7b922.zip (checked today: 01/07/13)
My main problem is that "NGS:Mapping section" does not look similar to the main
Galaxy page.
The downloaded package
Hello,
The next GalaxyAdmins Meetup will be Wednesday, January 16, 2013 from 10 AM to
11 AM US Central time. John Chilton of the Minnesota Supercomputing Institute
will cover "Deploying Production Galaxy Environments on OpenStack with
CloudBioLinux and CloudMan". You can join the meetup at
I am a little paranoid that I am the one that broke something (I guess
that is pattern matching more than paranoia), but I have looked
through that code and it is not immediately obvious to me what the
problem is. If you have some time, can you try cloning the workflow
and ripping various parts out
Hello All,
I'm trying to deploy my instance of Galaxy in production. Some tests
we've done show that when the number of person connected is high (>20
together), the server stops itself.
Sometimes, I have this error in the paster.log:
Exception happened during processing of request from ('12
This is really helpful,
Works great.
Thanks,
Hagai
On Mon, Jan 7, 2013 at 5:13 PM, John Chilton wrote:
> I am pretty confident there is no way to do this via the API
> currently, though I imagine it wouldn't be terribly complicated to add
> and the community would appreciate the contribution. I
Ok,
thanks for this information.
Cheers,
Cyril
On 01/08/2013 01:58 AM, Jeremy Goecks wrote:
These bugs have been fixed in our development repository
(galaxy-central) and will be available in the next distribution, which
should occur in the coming week.
Thanks,
J.
On Jan 7, 2013, at 6:23 A
Hi Ted,
This looks like a good solution to me. I'll add your contributions to the
Galaxy code base as soon as I get a chance.
Thanks for all of your efforts on this!
Greg Von Kuster
On Jan 7, 2013, at 3:22 PM, Ted Goldstein wrote:
> Hi Greg and James,
> This has become a plumbing project.
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