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,
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
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
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
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
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 view
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
ngsbioinformat...@gmail.comwrote:
I re-uploaded 3 BAM files using the Upload system
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
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
excellent, thanks for the correction!
On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi pa...@uab.edu 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
Hi Dannon,
On Wed, Jan 18, 2012 at 3:32 PM, Dannon Baker dannonba...@me.com wrote:
On Jan 18, 2012, at 12:20 PM, Carlos Borroto carlos.borr...@gmail.com 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
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 louise-amelie.schm...@embl.de:
Hello!
I'm running into an error when trying to download a composite dataset from
the
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
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,
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