On 02/03/2011 07:35 PM, Greg Von Kuster wrote:
Hello Jean-Baptiste,
Running the latest revision in the distribution, (4895:ad933d160a7c),
I have followed your steps precisely and do not see the behavior you
state.
Hello,
thank you for having trying to reproduce my problem. I've updated my
Ryan Golhar wrote:
I've implemented the Serving Galaxy at a sub directory (such as
/galaxy), made the change to Apache, and the universe_wsgi.ini.
When I view the page through Apache using http://server.name/galaxy,
the page is garbled like something didn't take.
Hi Ryan,
Did you
Ryan Golhar wrote:
SOLVED. I copied/paste the Rewrite rules for apache from the wiki
without updating the paths to my installation...once I did that, all
worked well.
Whoops, I should read ahead before I reply. Glad it's working!
--nate
On 2/17/11 5:07 PM, Ryan Golhar wrote:
I've
Ryan Golhar wrote:
Nevermind (once again). I figured out I need to compile it from the
torque...
You can also use the 'pbs' job runner, which wraps the PBS C API
directly instead of using DRMAA.
--nate
On 2/17/11 10:30 PM, Ryan Golhar wrote:
I'm configuring my local install of galaxy to
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my
cluster integration tomorrow. For now, I can see galaxy from my web
browser.
First issue - When I go to User - Login and try to log myself in
(I've
Ok, I don't know what happened with this...I reinstalled from scratch
and i seems to be working now. I suspect perhaps because I started
galaxy a few times before migrating to mysql. This time, I deleted
everything, changed the config settings then started galaxy.
I'm now on to testing my
I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs
getting submitted to Torque however the jobs keep failing, because the
tools are in the default system path.
How do I tell galaxy to append a directory to the path used by jobs?
--
CONFIDENTIALITY NOTICE: This email
Ryan Golhar wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I can see
jobs getting submitted to Torque however the jobs keep failing,
because the tools are in the default system path.
How do I tell galaxy to append a directory to the path used by jobs?
Hi Ryan,
Whatever
Hi,
I had same problem since we do not install software in the system directory. I
had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know
if anyone has better solution.
Zhibin Lu
Bioinformatics Support
Ontario Institute for Cancer Research
MaRS Centre,
It turns out the user's environment is not set up for batch jobs, only
the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break if/when the drmaa.py
file gets updated. It'll work for now, but there has got to be a
Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs,
only the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break if/when the drmaa.py
file gets updated. It'll work for now, but
On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs, only
the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break if/when the drmaa.py
file gets
On 2/18/11 2:37 PM, Glen Beane wrote:
On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs,
only the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break
All:
I retested under IE7 and found the bugs you were mentioning. This has all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golha...@umdnj.edu wrote:
Ok, I don't know what happened with this...I reinstalled from scratch and ...
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py, line
16, in ?
...
File
Hi all - I'm uploading datasets into my local instance by importing from
the filesystem w/o copying into Galaxy.
Importing of uncompressed files works properly. The files I'm importing
are owned by user1 and a read-able by everyone, including the galaxy
user. The galaxy user does not have
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