Just to add for the list, nate mentioned on IRC that running tests on an
external server likely doesn't work at the moment but that
./scripts/functional_tests.py may have something to work with via environment
variables.
chris
On Jan 18, 2012, at 8:03 PM, Fields, Christopher J wrote:
> Greg,
Greg,
That seems to work mainly for running tests from the sample universe/tool
config files, so it uses the local job runner. What I would like to do is run
tests using the actual Galaxy server configuration (which might use PBS/DRMAA
and a cluster). The method I mention from that page seeme
Hi, L-A
Thanks for reporting this - I just pushed a fix in galaxy-central
6556:ab1a5ab063ce
Please let us know if that resolves the problem?
2012/1/19 Louise-Amélie Schmitt :
> Hello!
>
> I'm running into an error when trying to download a composite dataset from
> the history with the floppy dis
perhaps a 15sec sleep should also be added, since the scheduler is
overwhelmed
{{{
except ( drmaa.DrmCommunicationException ), e:
# Catch drmaa communication exception, log a warning message and
# continue to monitor jobs.
log.warning("(%s/%s) Couldn't communicate with the cluster scheduler
Hi all. I'm sorry if this has been answered before, but I've searched and
cannot find a solution other than "add SAMtools to your PATH", which I
already have done. I can invoke samtools from BASH while logged in as the
"galaxy" user I set up according to the production installation guide. When
I tr
Hello Chris,
You should be able to run functional tests from the Galaxy install directory
using the following from the command line.
%sh run_functional_tests.sh
There are several options you can use as well.
Greg
On Jan 18, 2012, at 4:38 PM, Fields, Christopher J wrote:
> I have been followi
I have been following the basic protocol for running remote tests on a Galaxy
server (in this case, our local one) using:
http://wiki.g2.bx.psu.edu/Admin/Running%20Tests
>From reading this, I assume the tests are to be run from the galaxy root
>directory, like so:
GALAXY_TEST_EXTERNAL=1 GAL
Hi Dannon,
On Wed, Jan 18, 2012 at 3:32 PM, Dannon Baker wrote:
> On Jan 18, 2012, at 12:20 PM, Carlos Borroto wrote:
>
>> Hi,
>>
>> I was wondering if is possible to pass runtime values to workflows
>> thought the API? I want to run the same workflow for several inputs,
>> but there are values
excellent, thanks for the correction!
On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi wrote:
>
> Ed,
>
> I think you may want to add job with DrmCommunicationException error
> back into the watched_jobs list.
> {{{
> except ( drmaa.DrmCommunicationException ), e:
> # Catch drmaa communicati
>
> it works fine on the public server
Good, this narrows down the problem to installing the -central script on your
instance b/c main's copy of the script is very similar to -central's.
> what do you mean by "packed Trackster script"
All JavaScript files are compressed in size--comments/white
On Jan 18, 2012, at 12:20 PM, Carlos Borroto wrote:
> Hi,
>
> I was wondering if is possible to pass runtime values to workflows
> thought the API? I want to run the same workflow for several inputs,
> but there are values other than the inputs that I need to change for
> each run. Is it possibl
Hi,
I was wondering if is possible to pass runtime values to workflows
thought the API? I want to run the same workflow for several inputs,
but there are values other than the inputs that I need to change for
each run. Is it possible to leave these values as 'To be set at
runtime' and set them thr
Nate - Is there a specific place in the Galaxy code that forks the samtools
index on bam files on the cluster or the head node? I really need to track
this down.
On Fri, Jan 13, 2012 at 12:54 PM, Ryan Golhar
wrote:
> I re-uploaded 3 BAM files using the "Upload system file paths.
> runner0.log s
Ah, following the lead in the log paid off. I had to add the statement
*XSendFilePath
/panfs/galaxy_data *to /etc/httpd/conf/httpd.conf. Apparently ever since I
had moved the dataset directory to /panfs/galaxy_data by setting the
"file_path" variable in universe_wsgi.ini I have not attempted to vie
I seem to be getting somewhere by monitoring the /var/log/httpd/error_log
file (I don't know why I didn't think of that before). For each dataset I
click I am seeing a corresponding message like this:
*[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(56): proxy: HTTP:
canonicalising URL //local
Hello!
I'm running into an error when trying to download a composite dataset
from the history with the floppy disk icon. Here is the error message in
the logs:
galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to
remove temporary library download archive and directory
Tra
Hi Jeremy
A couple questions:
(a) What browser/OS are you using when seeing this problem?
chrome and firefox on Linux as well as firefox on Mac (10.5.8)
(b) Can you replicate this behavior on our public server?
it works fine on the public server
A couple notes: depending on your Web
Hans,
A couple questions:
(a) What browser/OS are you using when seeing this problem?
(b) Can you replicate this behavior on our public server?
A couple notes: depending on your Web server setup, it may be necessary to use
the packed Trackster script rather than the full one. Also, we're plann
Hi Jeremy,
Thanks for your effort, but when I cloned the dataset you shared with
me and switched it as current history, I still got
"Error executing tool: 'hg19'",
after I tried to run Cufflinks on both Tophats, on single and pair end data.
All best,
Milos
On Wed, Jan 18, 2012 at 1:47 AM, Jer
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