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 m
Tena Sakai wrote:
> Hi Nate,
>
> I am still not there, though I am getting closer...
>
> I changed the port to in universe_wsgi.ini and
> Here's what appears on my screen:
> galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval
> exceptions' middleware
> galaxy.web.buildapp
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
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:
>
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 galax
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 cl
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?
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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
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 user
Ryan Golhar wrote:
>
> >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 pat
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, Sou
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,
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
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 brea
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 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
> "/home/galaxy/galaxy-dis
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 wr
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li wrote:
> 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 tha
Can I sort (chr) bam file in Glaxay or I have to go back to samtools please?
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