XGrid is a dead-end technology. It has been removed from OS X starting
with Mountain Lion (10.8).
--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153
On 11/22/12 9:47 PM, James Boocock smilefreak2...@gmail.com wrote:
Hi Galaxy Dev Team.
We are looking to put
I really want this for Torque/Moab where the native spec flag is -A
Sent from my iPhone
On Jan 20, 2012, at 7:34 PM, Edward Kirton eskir...@lbl.gov wrote:
Great idea, Nate (hint! hint!).
On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote:
Hey Ed,
This is a neat
You aren't the only one having problem in the disk-usage reported in the upper
right. I've also had problems with this total disk usage in our local instance
of Galaxy
I've deleted all but a handful of files, and we have a cron job that purges the
files from disk after a certain number of
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
I have an mpileup tool for Galaxy I've developed. After a little more testing
I may be able to share it.
the tool also converts the bcl output of mpileup to vcf
On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote:
Hello David,
An update is planned, but we can't provide an exact time-line
On Oct 5, 2011, at 2:25 PM, Roy Weckiewicz wrote:
Hi,
We have a local galaxy instance running on mac osx connected to a mysql
database. We are having an issue downloading files which are 2Gb. I've read
posts on this mailing list that mention that there is a browser limit on
On Sep 27, 2011, at 1:14 PM, Nate Coraor wrote:
Glen Beane wrote:
We recently updated to the latest galaxy-dist, and learned that the
sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files
instead of the samtools merge wrapper sam_merge.py.
this is a problem for us
We recently updated to the latest galaxy-dist, and learned that the
sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files instead
of the samtools merge wrapper sam_merge.py.
this is a problem for us because MergeSamFiles.jar does not honor $TMPDIR when
creating temporary file
When you delete something in Galaxy it isn't purged from disk immediately
On Sep 16, 2011, at 6:32 PM, Candace Seeve little_se...@hotmail.com wrote:
I've deleted all of my histories and datasets and the status bar in the top
right corner indicates that I am using 67% of my quotas. Is there
to job by TORQUE.
From: Glen Beane [mailto:glen.be...@jax.org]
Sent: Tuesday, September 13, 2011 5:00 PM
To: Chorny, Ilya;
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Passing the number of mpi processors to SGE from xml
file
I think
On Sep 14, 2011, at 2:07 PM, Chorny, Ilya wrote:
It’s easy to hard code in the ini but I want to be able to set the number of
processors as a parameter.
that would be a nice modification to galaxy. I've always wanted parameterized
job runners, so I could include variables in a job runner
On Sep 13, 2011, at 6:01 PM, Oleksandr Moskalenko
o...@hpc.ufl.edumailto:o...@hpc.ufl.edu wrote:
I need to get Galaxy to use tools that are not located in the system path. At
the command line I can export the PATH either manually or with environment
modules 'module load foo'. However,
I think with the current state of Galaxy this would need to be fixed. You
would need to hard code the number of processors in the xml wrapper and in the
corresponding job runner for that tool
From: galaxy-dev-boun...@lists.bx.psu.edu
We are in need of a galaxy upgrade (we missed the last galaxy-dist update at
the end of June). However, we don't want to update to a 2 month old release
only to have a new release come out shortly after. Could someone on the
development team give me an estimate of when the next galaxy-dist
On Aug 12, 2011, at 7:42 AM, Peter Cock wrote:
On Fri, Aug 12, 2011 at 12:28 PM, Glen Beane glen.be...@jax.org wrote:
to compile these from source you'll want to grab the BLAT
source code from here: http://users.soe.ucsc.edu/~kent/src/
It looks like these are two different URLs
just wondering if anyone else in Galaxy land was having this problem, I
emailed tophat.cufflinks@ to let them know
We have been experiencing segmentation faults with cufflinks 1.0.3. Our
platform is CentOS 5.5, and we compiled from source using gcc 4.1.2 (Red Hat
4.1.2-48).
The
I should preface this by saying we are running a galaxy-dist that is a couple
months old now (we are planning on updating soon), but here is an annoying
issue we are seeing managing data library permissions:
The Roles not associated lists are filtered so it shows only roles associated
with
I just checked,
Using the User-Register menu works, however we require our users to log in so
when they go to galaxy.jax.orghttp://galaxy.jax.org they are redirected to a
login page if they are not already logged in. That page has the text This
installation of Galaxy has been configured such
You need a wrapper to capture the stderr
It would be nice if there were an option to base a tools status on the unix
return value (for well behaved programs)
On May 26, 2011, at 8:36 AM, shashi shekhar meshash...@gmail.com wrote:
Hi all,
I am using one tool which gives stdout and stderr
On Apr 15, 2011, at 7:15 AM, Glen Beane wrote:
I have been having trouble uploading a large number of fastq files to a
library (180). I am uploading a directory of files, and I am not copying the
files into Galaxy.
When I try to view the files in the library after uploading it takes
On Apr 8, 2011, at 11:01 AM, Dave Walton wrote:
This is very close to our config, except -
We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise
Server 11 (x86_64) with 16 GB of memory.
Instead of SGE our HPC cluster uses Torque/Moab for scheduling.
Also, we've
On Mar 30, 2011, at 8:34 AM, Kostas Karasavvas wrote:
Hi Glen,
Good to know. I assume that currently that is not happening though,
right? If yes, is it in your immediate plans?
It should happen now - each step in the workflow would get submitted as a
separate job to the cluster. At
On Mar 10, 2011, at 12:24 PM, Peter Cock wrote:
Hi all,
Via the Galaxy admin interface, I'm currently importing some BAM
files into a library from the local file system. Since they are big, I
don't want Galaxy to copy them.
So I looked at the Copy data into Galaxy? option and made
sure
how you solved the issue.
Thank you for your patience!
Best,
Jen
Galaxy team
On 12/27/10 6:22 AM, Glen Beane wrote:
On Dec 22, 2010, at 3:26 PM, Glen Beane wrote:
one of our users is experiencing this error from the SAM-to-BAM tool:
Error extracting alignments from
(/hpcdata
We run a local galaxy instance with multiple galaxy web servers and a job
runner. Per the wiki suggestion we have two config files:
universe_wsgi.webapp.ini and universe_wsgi.runner.ini. I've noticed that we
still need universe_wsgi.ini or else galaxy will not start
Instead of maintaining
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 Feb 9, 2011, at 9:44 AM, Glen Beane wrote:
I've been doing some testing with a Galaxy instance running on my laptop for
some tools we are developing. I am uploading a file into Galaxy from a URL
to use as test input (~1.5GB tabular) I can download this file to my laptop
in ~30 seconds
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