On 06/12/2014 12:06 AM, John Chilton wrote:
If anyone out there has tired using Galaxy with strictly MyISAM tables
and found it untenable - by all means please chime in.
Well, due to several reasons we are (still) using MySQL (version:
5.1.69) with only MyISAM tables. We have been
I've setup galaxy to submit jobs to our HPC cluster as the logged in user. I
used the drama python module to submit the jobs to our moab server.
It appears that the working directory for a submitted job is being removed by
galaxy prior to the job completing on the cluster.
I can see a
Hi,
I have configured to use the hierarchical object store but as soon as I try
to reset the filetpye of a dataset Galaxy is crashing with:
galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend
'files3' for creation of MetadataFile 5963
132.230.153.57 - - [12/Jun/2014:14:39:20
Hey Stephen,
Not a true solution, but I solved a similar issue (missing history pane)
by clearing out the browser cache.
Geert
On 06/10/2014 04:39 PM, Dannon Baker wrote:
Hey Stephen,
Can you look in the server logs to see if there are any errors being
reported? Or if there are any
Hey Hans (and anyone else using MySQL),
Just to clarify -- MySQL doesn't have this (particular) error by default
and as long as your server default table type has not and does not change
you should be fine. I've just successfully tested MySQL using MyISAM all
the way to the current tip revision
Thanks to everyone for their input.
John, your explanation was excellent. I completely agree with the
implementation of galaxy as it stands now (with a minor documentation warning
about default mysql engine switch in v5.5). Personally, I either place trust
in the ORM to maintain referential
Hey Donny,
What is the value of keep_completed on your queue (from qmgr -c 'p
s')? Could it be that your spool is flushing completed jobs
immediately? I ran into issues the other day with libdrmaa requiring
at least keep_complete = 60 seconds to properly detect completed jobs
and clean up after
Hi Eric,
It's not broken per se but the documentation is lacking on this front. You
need to route your /galaxy/api folder to a proxy that does not require
authentication. Maybe this isn't the best way but it works for AAFC's
production galaxy. See my apache configuration file below:
job_conf.xml is outside of my knowledge. Better wait to see what the
others can tell us.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Thu, Jun 12, 2014
Vipin,
I've attempted to duplicate this error locally, with no luck as yet.
Would you be able to send me the specific tar.gz file that was causing
problems?
--Dave B.
On Wed 11 Jun 2014 05:02:34 PM EDT, Vipin TS wrote:
Hi Greg,
Please find the attached screenshot from my side. The same
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Hi Iyad,
Thanks for posting configs! I'm very curious how this actually works for
you.
I'm running the API scripts from the galaxy server itself, and I made
requests to http://fqdn/galaxy/, http://localhost:/, and
http://localhost:/galaxy/
Hi Björn,
I believe the problem is most likely this bug:
https://trello.com/c/OHlQoCrx
If you symlink /usr/local/galaxy/galaxy-dist/database/tmp to somewhere
writeable (e.g. what you have new_files_path set to), that'd confirm it.
I'm going to take a look at fixing this today.
--nate
On
Hey Eric,
I am pretty sure Iyad's configuration is right - here is a similar
config for nginx with some discussion of the API problem
http://production-galaxy-instances-with-cloudman-and-cloudbiolinux.readthedocs.org/en/latest/#external-authentication-ldap.
It is fine if it is empty it just has
Hi Nate,
yes that is fixing it for me!
Thanks!
Bjoern
Am 12.06.2014 16:26, schrieb Nate Coraor:
writeable (e.g. what you have new_files_path set to), that'd confirm it.
___
Please keep all replies on the list by using reply all
in your
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Hi John,
Seems like odd behaviour, but if that's how it works, then that'll
adequately fix my problem.
Thanks John/Iyad!
Cheers,
Eric
On 06/12/2014 09:40 AM, John Chilton wrote:
Hey Eric,
I am pretty sure Iyad's configuration is right - here
My guess is Galaxy is deleting the directory because it believe the
job is in error because of some communication problem while polling
your DRM via DRMAA - Galaxy thinks the job has failed before it has
even been run.
You can set
cleanup_job = never
in universe_wsgi.ini's app:main section to
Hi John,
That did the trick. I have some other problem but I don't think it's galaxy
from here.
Thanks again for the reply.
Donny
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: Thursday, June 12, 2014 10:53 AM
To: Evan Bollig
Cc: Shrum, Donald C;
Hello,
I'm getting an error with fastx tools on a local install of galaxy. From this
error I can't tell if it's a problem with the file, database, or tool.
An error occurred with this dataset: zcat:
/Volumes/Jose-Drobo/galaxy-dist/database/files/002/dataset_2875.dat.Z: No
such file or
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Today I tried to access my org's toolshed, only to realise that it
wouldn't load as it was behind the firewall. Since I'm not in the mood
to connect my VPN, I thought I'd posit the following:
Perhaps the galaxy server should make the HTTP requests to
Hi all
I gather that it is NOT allowed to assign multiple file to from_file
attribute for options in select param as the expect value of from_file
attribute is the name of A file. But would it be nice to allow this feature?
For example, there are two loc file A and B, when I want to get
Hello,
when i run my galaxy instance type:
$ sh run.sh
I get some error like this:
Traceback (most recent call last):
File /export/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 38, in
app_factory
from galaxy.app import UniverseApplication
File
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