Hi Carl,
Thank you for your quite extensive answer! I finally managed to find the line
in universe_wsgi.ini that caused the problem.
The moment I UNCOMMENT the following line:
#log_actions = True
I no longer can see the histories. The moment I comment this line again
everything works fine.
Many thanks for the observation. This will come handy next time I hit the same
rock. I hope not so soon.
Ambrose
-Original Message-
From: Groot, Philip de [mailto:philip.degr...@wur.nl]
Sent: 16 July 2013 12:03
To: Carl Eberhard
Cc: galaxy-dev@lists.bx.psu.edu; Ambrose Andongabo
Hey guys,
i was searching the mailing list and wiki for some hints if there is a
possibility to enhance the repeat tag.
We want to give the option to our users to add more than one additional set of
the contained parameters at one go e.g. 10 or 20 or 50, because it can be very
frustrating to
Oops, I was replying via theGalaxy Development List Archive
http://dev.list.galaxyproject.org/ interface, strange it has put the
reply off list...
So no functional test for my tool ( despite my enthousiasm :-) ), since
the repeat tags must be provided in the test.
Thanks,
Joachim.
Joachim
OK, it seems that the current state of the functional test framework
'simulates' one click on the 'repeat' button. You just provide one set
of param names contained within the repeat block. Luckily, this is
enough for my tool now.
Cheers,
Joachim
Joachim Jacob
Contact details:
Hi there!
Is there an easy way to pass a users group associations to a tool as a
parameter. Maybe similar to pass user information via the reserved
variable $__user_email__ ?!
I tried $__app__.model.UserGroupAssociation.group however I end up
with a mapper-object and are kind of stuck
Dear Madam/Sir,
I have installed Galaxy Local in our system. I registered as a user. However
when I try to give admin status to some users, I am unable despite following
the steps mentioned in the help.
To give a user Galaxy admin privileges, add their Galaxy login ( email ) to
the list in
Hi
Just double checking: Have you restarted Galaxy?
Regards, Hans-Rudolf
On 07/16/2013 07:23 AM, Chadi Abdul Kader El Farran wrote:
Dear Madam/Sir,
I have installed Galaxy Local in our system. I registered as a user. However
when I try to give admin status to some users, I am unable
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to
create your instance, it should display an example connection string that will
work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem
ubuntu@IP', after your instance launched.
Once
I like your proposal. I don't think it is currently possible to add -
say - 5 repeat blocks at once. Feel free to add and describe your
suggested enhancement on Trello, so I can vote for it :-)
http://galaxyproject.org/trello
Cheers,
Joachim
Joachim Jacob
Contact details:
Rather than adding additional increments to add/remove, what about
allowing the user to directly set the number of elements in the
repeat?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 16, 2013 at 7:34 AM, Berner, Thomas
thomas.ber...@jki.bund.de wrote:
Hey
Hello,
I found a couple of issues in using the latest version of Cloudman
(revision:10201:ebe87051fadf).
The Extract Genomic DNA tool returns an error:
No sequences are available for 'mm9', request them by reporting this
error.
Upon trying to report the error in Galaxy (on the page that comes up
Hey Mo,
The new volume we pushed out for the conference has several known issues.
Enis and I are both away from the office on travel right now, but updating
the volume and fixing these issues is the first thing I'll be doing when
I'm back next week.
For now, you can launch using the
Dear All,
We have had a working local galaxy instance being used with mySQL for almost
two years with a lot of new scripts, workflows built-in and datasets still
associated with it.
We now would like to move to a new server but rather than start from scratch,
would like to move all parts of
I've had success using the pbs runner rather than drmaa runner for this
case. It's quite straightforward to specify the pbs_server for the pbs
runner. Works just as the documentation indicates.
- Bart
On Tue, Jul 9, 2013 at 1:46 PM, Bart Gottschalk bgott...@umn.edu wrote:
I haven't been
Thanks guys! I'm going to try it out now.
Would you mind letting me know when the issues are fixed next week?
(updating this thread would be fine)
Thanks again,
Greg
On Tue, Jul 16, 2013 at 12:42 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Greg,
We put together a quick workaround
Are there any plans in the works to support plugins within Galaxy? One of the
tools I'm working on is actually more of an extension of the workflow
canvas/editor's user interface. Right now, I've minimized the modifications
required to the editor.mako file to simply adding a mako include near
James,
That's exactly what I was thinking. In my opinion, hooks are the way to go (as
seen in my example), but if there's a better way then I'm game for that to. I
just want to be able to extend Galaxy without modifying Galaxy itself.
Thanks!
Sincerely,
Michael E. Cotterell
Ph.D. Student
Michael,
Galaxy is all about plugins! Tools, datatypes, batch systems,
visualizations, et cetera.
Additional ways to extend Galaxy through plugins are very welcome. We
just need to make sure that whatever solution is chosen is extremely
general.
--
James Taylor, Assistant Professor, Biology/CS,
On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote:
One of my goals for the GCC was to sell the idea that tool shed
repositories need to be installable without a database present. I
John, as I've mentioned in the past I'm very strongly in favor of
this. There is
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
have to choose a bioinformatic pipeline management tool to find SNP's in
genomes from hcc patients. My decision was made in favor of galaxy. I have
a 64-bit openSuse 11.3 server.
I have installed
Hi Team,
I am attempting to rebuild my local instance of galaxy on my Mac since having
been upgraded to Mountain Lion. I have installed Mercurial, postgres,
python2.7. I have cloned the latest galaxy-dist. However, when I attempted to
launch galaxy with sh run.sh it fails to complete the
Hi.
Getting error when trying to install the latest Galaxy on a new stand alone
linux RH server. Is the repository down?
migrate.versioning.repository DEBUG 2013-07-16 14:14:46,235 Config:
{'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]',
'version_table': 'migrate_tools',
Nice catch!
I'll see where this leads.
On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de philip.degr...@wur.nlwrote:
Hi Carl,
Thank you for your quite extensive answer! I finally managed to find the
line in universe_wsgi.ini that caused the problem.
The moment I UNCOMMENT the following
On Tue, Jul 16, 2013 at 1:16 PM, James Taylor ja...@jamestaylor.org wrote:
On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote:
One of my goals for the GCC was to sell the idea that tool shed
repositories need to be installable without a database present. I
John, as I've
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