Thanks, Nate,
I now switched to MySQL, and the problem disappeared. Thanks.
The manual highly recommend postgresql, is there any critical point to
use it, instead of mysql? I am just more familiar with mysql. Thanks.
On Wed, Jan 4, 2012 at 1:58 AM, Nate Coraor n...@bx.psu.edu wrote:
On Dec 29,
Dear All,
First of all, we wish you all a happy new year!
Sending this (see below) again in case it slipped in the rush before X-mas.
Best wishes,
Tim, Soon and Mesude
--
Dr. Mesude Bicak mbi...@ceh.ac.uk
Bioinformatician Bio-Linux Developer
NERC Biomolecular Analysis Facility (NBAF)
Dear all,
I’m using the online version of Galaxy (I’m just a user, not a
developer) and I think that there might be a problem with the output
of Megablast. Indeed, I’ve noticed that the GI of the database hit
(given column 2 in the output table) is not in agreement with the
details given in the
Hi Carlos,
Yes, I'm an active member of Deb Med but unfortunately not finding time
to read the mailing list properly nor to actually run Debian (or even
the Ubuntu development release).
We've actually factored time into the packaging project to contribute
all relevant packaging into the
Hi Derrick,
I would first try changing your test URL:
http://www.publicnet.org/galaxy
to be:
http://publicnet.org/galaxy
If this doesn't work, let us know the error - these proprietary configurations
are tricky to figure over email, but we'll try to help.
On Jan 4, 2012, at 11:11 PM,
The manual highly recommend postgresql, is there any critical point to
use it, instead of mysql? I am just more familiar with mysql. Thanks.
The Galaxy team has found that, when running Galaxy, postgres is more stable
and robust than mysql. Also, we use postgres ourselves, so it's
Efthymois,
You'll want to run Galaxy as a daemon process. Run
% sh run.sh --help
to get more information on running Galaxy as a daemon.
Also, please direct questions about running/configuring a local Galaxy instance
to galaxy-dev (cc'd) rather than galaxy-user, which is for tool and analysis
On Jan 4, 2012, at 5:31 PM, Carlos Borroto wrote:
On Wed, Jan 4, 2012 at 12:59 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Hi,
While trying to import some fastq files to a data library, using
Upload directory of files and Link to files without copying into
Galaxy, I end with empty
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.com
wrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.com
wrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this
by importing directories that contain bam and bai files. I see the bam/bai
files get added
On Jan 5, 2012, at 11:29 AM, Ryan Golhar wrote:
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.com
wrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain
OK. Thank you all.
On Thu, Jan 5, 2012 at 9:32 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
The manual highly recommend postgresql, is there any critical point to
use it, instead of mysql? I am just more familiar with mysql. Thanks.
The Galaxy team has found that, when running Galaxy,
Dear all,
I would like to get the latest copy from the repository
(https://bitbucket.org/galaxy/galaxy-dist) in order to install Galaxy.
But, unfortunatly, no server is available to handle this request (503
Service Unavailable).
Could you, please, help me ? Do you know when this information
On Jan 5, 2012, at 10:52 AM, sarah Maman wrote:
Dear all,
I would like to get the latest copy from the repository
(https://bitbucket.org/galaxy/galaxy-dist) in order to install Galaxy.
But, unfortunatly, no server is available to handle this request (503 Service
Unavailable).
Could you,
I set it to run on the cluster:
[galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini
#upload1 = local:///
On Thu, Jan 5, 2012 at 11:33 AM, Nate Coraor n...@bx.psu.edu wrote:
On Jan 5, 2012, at 11:29 AM, Ryan Golhar wrote:
On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
On
Do you mean this (In universe_wsgi.ini)?
...
# Debug enables access to various config options useful for development and
# debugging: use_lint, use_profile, use_printdebug and use_interactive. It
# also causes the files used by PBS/SGE (submission script, output, and error)
# to remain on disk
On Jan 5, 2012, at 11:41 AM, Ryan Golhar wrote:
I set it to run on the cluster:
[galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini
#upload1 = local:///
Could you set use_heartbeat = True in the runner's config file and then check
the resulting heartbeat log files created in
On Jan 5, 2012, at 11:46 AM, Ryan Golhar wrote:
I have three bam files that I'm trying to merge. The job runs for a bit
then errors saying there is a problem. When I look at runner0.log I see:
galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting
file
Hello all,
The documentation is on my todo list, and is fairly high up on it (and now
it's a little higher). However, it is a wiki and everyone is encouraged to
create an account and update the doc as you learn things.
Dave C.
On Wed, Jan 4, 2012 at 1:34 PM, Nate Coraor n...@bx.psu.edu wrote:
Ivan,
#if $__user_email__ ==
displayYou are not authorized to use this tool/display
#else
command interpreter=python
data_source.py $output $__app__.config.output_size_limit
/command
To make this approach work, the email check should go in the command tag.
More
I discovered the problem. My pbs queue has a wall time restriction of
3600 seconds.
Is there a way to configure Galaxy to keep the job files for only failed
jobs? I'd like to keep these two settings on, but find it unnecessary if
jobs successfully complete.
The other option I would
In recent versions, the setting in the Galaxy config to keep job files is:
cleanup_job = never
I discovered the problem. My pbs queue has a wall time restriction of 3600
seconds.
Is there a way to configure Galaxy to keep the job files for only failed
jobs? I'd like to keep
On Jan 5, 2012, at 1:10 PM, Ryan Golhar wrote:
I discovered the problem. My pbs queue has a wall time restriction of 3600
seconds.
Is there a way to configure Galaxy to keep the job files for only failed
jobs? I'd like to keep these two settings on, but find it unnecessary if
Hello Jim,
I've implemented support for proprietary datatypes that use class modules
included in tool shed repositories. To see how this works, you'll need at
least change set revision 6479:4d131422777f, which is currently available only
from our central repo at
Hi Jim,
Here are the changes you'll need to make to your mothur tool suite.
CHANGE 1
Add the following datatypes.conf.xml file to your repository.
?xml version=1.0?
datatypes
datatype_files
datatype_file name=metagenomics.py/
/datatype_files
registration
Your approach is great since it models the Galaxy distribution, and as you say,
make sit clear to those downloading your repository. However, your datatype
class module files will be found no matter where they are located within your
repository hierarchy.
On Jan 5, 2012, at 3:25 PM, Jim
Of course, this assume that there is not more than one datatypes class module
in your repository with the same name. This would definitely pose problems, so
care should be taken that it is not done.
On Jan 5, 2012, at 3:29 PM, Greg Von Kuster wrote:
However, your datatype class module files
Yes, this is certainly important, but I think the hope is that proprietary data
types will not become so prevalent that name-spacing the extensions is
necessary.
On Jan 5, 2012, at 4:15 PM, Jim Johnson wrote:
Big Question?
When I started creating all those datatype classes for mothur,
Hi guys,
Thanks for the helps. I used http://publicnet.org/galaxy for visiting the
site, so it's my typo.
On Fri, Jan 6, 2012 at 3:49 AM, Carlos Borroto carlos.borr...@gmail.comwrote:
The fact your apache server is looking in /var/www/galaxy means the
'RewriteRule' is not working. Did you
Of course, your approach of prepending the repository name would probably
eliminate any future issue in this regard. Whatever you feel is best... ;)
On Jan 5, 2012, at 4:49 PM, Greg Von Kuster wrote:
Yes, this is certainly important, but I think the hope is that proprietary
data types
Good afternoon Galaxy list,
I've got a Python script which calls an R script. When I run a job using
Galaxy, I get the following output from R:
Error in file(file, r, encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(file, r, encoding = encoding) :
I haven't found a way to fix the status on BAM files being imported. They
still read Job still running. So I thought I'd just delete the whole
data library and start a new. From the Admin page, I click Manage Data
Libraries, then select all the data libraries by clicking the checkbox next
to
Hi Carlos,
You are right! I put the same config to site-available and now it works!
Will do more testing/configuring base on that.
Do you know why the location of the settings cause this issue?
Thanks
Derrick
On Fri, Jan 6, 2012 at 12:42 PM, Carlos Borroto carlos.borr...@gmail.comwrote:
On Thu, Jan 5, 2012 at 8:51 PM, Derrick LIN klin...@gmail.com wrote:
Hi Carlos,
You are right! I put the same config to site-available and now it works!
Will do more testing/configuring base on that.
Do you know why the location of the settings cause this issue?
I would have to read a
From the doc:
By default,
mod_rewritehttp://httpd.apache.org/docs/current/mod/mod_rewrite.html
configuration
settings from the main server context are not inherited by virtual hosts.
To make the main server settings apply to virtual hosts, you must place the
following directives in each
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