Jobs run as the condor user? That is surprising - Galaxy isn't running
as the condor user is it?
Is your intention to have the jobs run as the 'galaxy' user or to run
as the LDAP authenticated end-user submitting the job?
If it is to run as the Galaxy user - I think it would be best to have
condo
Our galaxy server has an apache front end with ldap authentication.
I've added a condor destination...
There are some tools I'd like to point to condor but it appears all the jobs
will be sent as the user condor.
Is there an existing fix that will submit jobs to our condor cluster as the
l
*We just released an update to Galaxy CloudMan.* CloudMan offers an easy
way to get a personal and completely functional instance of Galaxy in the
cloud in just a few minutes, without any manual configuration.
This is mostly an incremental bug fix release with the following summary of
changes:
On occasion I'm getting and 'Internal Server error' on login with my production
galaxy server.
If I refresh the page I'm able to login just fine.
This instance of galaxy has an apache frontend and a mysql server on the back
end. If I look at my log files I see:
OperationalError: (OperationalE
Hi Renato,
Am 05.08.2014 um 17:34 schrieb Renato Alves:
Hi Bjoern,
Thanks for the info and the fix.
So far we had no issues but it's not extensive testing. I'll let you
know if it fails for some reason.
In addition to the shebang change we also started using "perl script"
instead of simply "s
Ah, I think that I had a wrong impression before...so by default, the
migration scripts listed here will NOT be executed, am I correct? I think
that 'done' at the bottom made me think that it was executed...
So it's the user's responsibility to execute those scripts, correct?
Thanks,
Rui
The Emb
Bjoern,
I am not getting the same error. However, it is still failing. I get the
following banner:
This tool dependency is not installed correctly (see the Tool dependency
installation error below). Choose Uninstall this tool dependency from the
Repository Actions menu, correct problems if n
Ahh, I think I see the issue. So, many galaxy tools are being migrated out
of the distribution and to the toolshed -- you can find much more detailed
information here:
https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
The samtools wrappers were migrated in migration 8, I think,
Hi Dannon,
Thanks for the reply. Sorry for the duplicate. I was wondering that the
original subject sounded like a user problem so I updated it...
Actually we are having a little down time right now for a file system
check. I'll try your suggestions asap and let you know. At the mean time,
could
Hi Rui,
We'll definitely take a look. Please allow for a reasonable time period to
pass before sending duplicate emails to the list asking for assistance.
That said, does deleting your integrated_tool_panel.xml (this file is
automatically regenerated by Galaxy, safe to remove it and restart) bri
Iry,
are you seeing the same error with:
https://toolshed.g2.bx.psu.edu/view/iuc/snpeff
Cheers,
Bjoern
2014-08-06 19:12 GMT+02:00 Iry Witham :
> Hi Greg,
>
> That resolved the internal server error issue. Now I need to figure out
> the issue with the dependencies. I was unable to post th
Hi Greg,
That resolved the internal server error issue. Now I need to figure out the
issue with the dependencies. I was unable to post the actual error message
previously, but am doing so now. Here is the error I get for the dependency
installation:
NameVersion TypeStatus Error
snp
Could someone please take a look?
Thanks,
Rui
On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI wrote:
> Dear Admin,
>
> Since the upgrade, I lost the samtools that I installed myself. Although
> it is still in the tool_conf.xml, it does not show up on the panel. I tried
> to install from toolshed, b
Hi Greg,
Could there be some problems with https://toolshed.g2.bx.psu.edu/ I have
some troubles installing toolshed tools in our galaxy. When I try
installing for instance 'suite_samtools_0_1_19', I am presented with a 500
error.
I tried then pulling a new stable galaxy from bitbucket, which see
Hi Iry,
Sorry for the inconvenience. The tool shed server was out of space - I've
corrected the problem and have successfully installed repositories. Please try
again and let us know if you encounter problems.
Thanks!
Greg Von Kuster
On Aug 6, 2014, at 12:20 PM, Iry Witham wrote:
> Hi Te
Hi Eric,
Sorry for the inconvenience. The tool shed server was out of space. I've
corrected the problem and have successfully installed repositories into my
local Galaxy instance. Please try again and let us know if you encounter
problems.
Greg Von Kuster
On Aug 6, 2014, at 10:59 AM, Eric
Hi Team,
I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed
and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue.
Once the installer completes it shows that the dependency snpEff.x.x was not
installed. When I try to install the dependency
Thanks for the help John and Dannon. I'll see if it works tomorrow. No need to
raise a trello card
Thanks
Neil
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, August 05, 2014 11:14 PM
To: John Chilton
Cc: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev
I had a similar issue a while ago. Greg mentioned the following setting
in universe:
# Enable use of an in-memory registry with bi-directional relationships
# between repositories (i.e., in addition to lists of dependencies for a
# repository, keep an in-memory registry of dependent items for ea
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