Chorny, Ilya wrote:
So it looks like for some reason galaxy is not picking up the information in
the .e file. Not sure why. I even switched it back to writing the files to
the pbs directory and it still did not pick up the .e files. BWA was core
dumping but I was not given the error message
Not currently, though I can put it on my list to try and add when I have a
chance.
-Dannon
On Nov 1, 2011, at 5:30 PM, Oren Livne wrote:
Dear Dannon,
Is there a web API method for deleting a data library? If not, what are the
chances of it being added soon?
Thanks so much,
Oren
On
Hi Jim,
I am going to post your question over to the galaxy-dev mailing list (is
best for local/cloud instance questions).
Would you be able to confirm which version of Galaxy you are running?
The latest version of the distribution?
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_10_25
Chorny, Ilya wrote:
I am pulling and testing as we speak. I did a preliminary test on my VM but
it does not have enough memory to run BWA. We pull into my dev version on the
cluster and do further testing. Also need to test how it integrates with the
splitting code. Should have some
Hello Devs,
I can confirm I am using the latest build:
galaxy@monolith:~/galaxy-dist$ hg pull -u -r 338ead4737ba
pulling from https://bitbucket.org/galaxy/galaxy-dist/
searching for changes
no changes found
galaxy@monolith:~/galaxy-dist$
Here is a copy of the error message that shows when I
Hey John,
Any thoughts?
Ilya
Traceback (most recent call last):
File /home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py,
line 73, in run_job
tasks = splitter.do_split(job_wrapper)
File
/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py, line
73,
The datatype you are using does not define a split method. Are you working with
our in-progress gz type or fastqillumina?
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
Dean, nginx integration works by proxying to the Paste server, but offloading
some data intensive parts. So you still need that configuration as it is.
Thanks!
-- jt
(composed on my phone)
On Nov 2, 2011, at 12:35 PM, Dean Snyder dean.sny...@jhu.edu wrote:
I switched from using the default
James, do you have an entry for the fasta_to_len convertor in your
datatypes_conf.xml? If not, you might want to update your config to include
those entries from the sample. Thanks!
-- jt
(composed on my phone)
On Nov 2, 2011, at 11:58 AM, James Vincent j...@uvm.edu wrote:
Hello Devs,
I
David,
Wrapper supports v1.0.0 to v1.1.0
I'll update the wiki momentarily.
J.
On Nov 2, 2011, at 2:04 PM, David Hoover wrote:
What version of cufflinks do the current Galaxy wrappers support? The wiki
(http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) says 1.0.1, but
our local
Cinto Queky wrote:
Hi All,
We encountered queuepool limit problem after running the workflows for a few
times.
We have tried to increase these 2 parameters:
database_engine_option_pool_size and database_engine_option_max_overflow to
20 and 40 respectively.
Are there other parameters
Shantanu Pavgi wrote:
Hi,
It seems like modification of 'citation_url' in the universe_wsgi.ini config
file has no effect in the UI (Help -- How to Cite Galaxy). Is it something
hard-coded in the source?
Hi Shantanu,
Whoops. This has been fixed in 6205:9a9479f7e53f.
--nate
--
Oren Livne wrote:
Dear All,
I am running the example_watcher_folder.py API script and it
intermittently fails to run a workflow on a file dropped into the
import directory (the file is imported and the workflow starts
running, but its jobs hang or fail). Galaxy uses a condor dramaa job
I'll submit a pull request shortly...
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: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
Sent: Wednesday,
On Nov 2, 2011, at 4:57 PM, Nate Coraor wrote:
Glen Beane wrote:
Many of us are using the PBS job runner (for TORQUE) and would definitely be
interested in a port.
Technically, using the drmaa runner with TORQUE is supposed to work. I
just tried it here to test Ilya's code, and Galaxy
On Nov 2, 2011, at 3:39 PM, Nate Coraor wrote:
Shantanu Pavgi wrote:
Hi,
It seems like modification of 'citation_url' in the universe_wsgi.ini
config file has no effect in the UI (Help -- How to Cite Galaxy). Is it
something hard-coded in the source?
Hi Shantanu,
Whoops. This
Hello:
The display tool for UCSC that comes with the local installation package
does not work. uploading a bigbed file (from the test-data that comes with
the package) does not trigger the webapp to show an option to view the file
using UCSC's viewer.
How do I enable this ?
To reproduce the
Hi Nate,
Yes, that was the issue. I just made sure that the cluster nodes are using
the same Python as the application server and it works now.
Thanks for the support.
Regards,
Jerico
On 3 November 2011 04:18, Nate Coraor n...@bx.psu.edu wrote:
Jerico Nico De Leon Revote wrote:
It's the
18 matches
Mail list logo
