Ok, Daniel I don't really know egg vs site-packages install or how to change
that; I tried upgrading our python 2.6 Paste to 1.7.5 but that didn't effect a
change. Dannon I tried toasting compiled_templates directory, to no avail.
The site was last upgraded in 2012. I'm afraid to mess with it
Hi all,
So I am trying to push our toolshed directories to our own repo and I am
running into problems. Basically, since the toolshed tools are subrepos, I
can't figure out how to push those changes into *our* repo. Also, I have
had to change some of the toolshed tools because they don't work prop
While testing an upgrade from latest_2014.10.06 to GitHub release_15.03
branch (cloned today) I ran into an issue trying to use the "Run this job
again" functionality on a dataset. I was playing with creating dataset
lists using "Operations on multiple datasets" and noticed that after adding
a data
Hi Martin,
We haven't upgraded to the March release yet, and I haven't really touched
the tools I referred to in my original email since I got them working
(despite the duplicate installation records in the admin interface, etc).
I've started testing the new release, though, and will take another
Hi Damion,
Another thing to try, is to set up and use a virutalenv, as the last time this
error was reported (2012), it was suggested that a local site-packages version
of Paste, instead of Galaxy’s provided egg, was to blame.
Thanks for using Galaxy,
Dan
On Apr 15, 2015, at 5:36 PM, Dannon
Hrmm, was worth a shot. And, I *think* the logic is such that this won't
change anything, but you can also (safely) wipe out that whole
compiled_templates directory and see if that does anything.
When you say old, just how old (hg summary) *is* this install? That might
give us a few tips.
On We
Darn, didn't change anything. I deleted them both as galaxy system account and
as root, but still that error on restart.
Thanks for this tip though.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for
Disease Control
655 West 12th Avenue, Vancouver, British Columb
Hi Damion,
I'm suspicious of the compiled templates. Can you disable debug, then do
something like "find /usr/local/galaxy/production/galaxy-dist -name '*.pyc'
-delete", and then restart?
-Dannon
On Wed, Apr 15, 2015 at 4:16 PM, Dooley, Damion
wrote:
> I have an OLDER Galaxy install I was goi
I have an OLDER Galaxy install I was going to fade out. In meantime I saw that
its debug flag should be turned off, so I did. But when it restarted it
complained in the history tab with a server error. I put debug back into
config and it runs fine. I haven't changed anything recently on it.
Hello all,
Just a reminder that oral presentation abstract submission for GCC2015
closes on Monday, 20 April, 5 days from now. Poster submission closes 1
May. See http://gcc2015.tsl.ac.uk/Abstracts for more.
The 2015 Galaxy Community Conference is an opportunity to share your work
with 200+ oth
Hello all,
Just a reminder that the April GalaxyAdmins online meetup is tomorrow,
Thursday, at 5pm Central European Summer Time. See
https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16
for details. A link to the meetup will be posted about an hour before the
meetup.
Thanks,
Hello,
I have a created an answer for this question in the planemo tool
development tutorial:
http://planemo.readthedocs.org/en/latest/writing_standalone.html#determined-the-user-submitting-a-job
From the docs:
The variable ``$__user_email__`` (as well as ``$__user_name__`` and
``$__user_id__``
Thanks John,
Jeremy, for another example see:
https://github.com/peterjc/galaxy_blast/issues/53
We have working tests using *.loc files, but they are currently commented
out for upload to the Tool Shed because they fail there :(
As far as I know, there isn't yet a Trello issue for fixing this on
Hi,
Is there a way to query the actual name of the user, who is logged into galaxy
and submitted the workflow ($REMOTE_USER), from inside a galaxy tool
when galaxy is configured for external authentication using an apache server?
It seems like galaxy passes this variable to scripts like
'drm
Hey Jeremy,
I have just updated the planemo tool development tutorial with an
answer to this question (I am trying to assemble something of a tool
development FAQ at the end of that tutorial):
http://planemo.readthedocs.org/en/latest/writing_standalone.html#test-index-loc-data
tl;dr - You can de
Hi Michael,
Am 07.04.2015 um 21:46 schrieb Michael Crusoe:
> On Wednesday, March 25, 2015, Björn Grüning
> wrote:
>
>> Hi all!
>>
>> We are proud to present you the next release of Galaxy Docker.
>>
>> https://github.com/bgruening/docker-galaxy-stable
>> https://registry.hub.docker.com/u/bgrueni
Hi Keith,
> Hi Björn,
>
> Thanks for the quick reply.
>
> It might help to take a look at what I have so far. Our Galaxy server is
> running at http://grid.anc.org:8000
> The front page contains a very basic tutorial (and I use the term loosely)
> with instructions for creating a simple wor
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