Hi,
I'm working on an local installation of galaxy using torque with drmaa
(the pbs-torque scramble failed). The torque-drmaa works fine so far,
except for one issue.
I'd like to specify some tool-dependent requirements from the
tool_runners section in universe.wsgi.ini. For now I've been te
Hi
default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/
works for me on LSF, so your syntax seems to be correct.
Assuming that -l mem=4gb:nodes=1:ppn=6 works teh way you expect when you
start the jobs on your cluster from the shell, read on...
Bearing in mind the the value of the op
Hi,
I ran into a little something that is a bit annoying for debug when
trying to upload files through the API with
library_upload_from_import_dir.py. When the specified folder is wrong,
python tries to process the error tuple like a dict, so the original
error is hard to find.
I modified a
Helo Ravi, please send all questions to one of the Galaxy mail lists as sending
to personal emails will usually not generate responses. I've forwarded your
question to the dev list since I am not involved in the Galaxy cloud
development efforts.
On Jun 17, 2011, at 5:47 PM, Sanka, Ravi wrote:
Hi Ravi,
CloudMan does handle the updates but it is not necessarily automatic.
Namely, once you create a Galaxy CloudMan instance, the settings and tool
versions used at that version will remain the same. If/when we release an
official update for Galaxy and/or tools, it is possible to point your
in
I'd like to have Galaxy and another application installed on the same Apache
server and have the user authenticate only once. I think I understand how to do
that by deferring authentication to Apache (instead of using Galaxy's built-in
database). So far, so good, I think.
What I'm wondering is
Hello John,
I'm not an apache expert, but I can try to help with some info.
your question involves two different issues, which are not dependent on one
another.
First, can one setup apache authentication that will affect both Galaxy and
other "things" on your server ?
The answer is yes.
Examp
Nate Coraor wrote:
> Matthew Conte wrote:
> > 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 i
Thanks! That's perfect.
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
-Original Message-
From: Assaf Gordon [mailto:gor...@cshl.edu]
Sent: Monday, June 20, 2011 12:09 PM
To: Duddy, John; gal
Hi,
We have a galaxy server setup using external shibboleth authentication. While
we would like to have site behind authentication realm, there are instances
when our galaxy datasets/histories need to be accessible publicly from other
websites. We tried adding an exception to auth rule for /dat
FWIW, Penn State uses Cosign for single sign-on, and I've successfully
placed Galaxy behind Cosign before (Cosign relies on Kerberos, and so
may not be a good fit at all sites). But as Assaf says, basically
anything should work.
--nate
Duddy, John wrote:
> Thanks! That's perfect.
>
> John Duddy
Shantanu Pavgi wrote:
> Hi,
>
> We have a galaxy server setup using external shibboleth authentication. While
> we would like to have site behind authentication realm, there are instances
> when our galaxy datasets/histories need to be accessible publicly from other
> websites. We tried adding
On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote:
> Shantanu Pavgi wrote:
>> Hi,
>>
>> We have a galaxy server setup using external shibboleth authentication.
>> While we would like to have site behind authentication realm, there are
>> instances when our galaxy datasets/histories need to be acc
Hello all,
I am Russell, a student working with Dr. Victor Jin at the Dept. of Biomedical
Informatics, OSU Medical Center. I am developing a Galaxy wrapper for our
ChIP-seq peak-calling program BELT (PMID: 21138948), and I have a question
about input validation. Does Galaxy filter for malicious
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