This is a reminder that the main ISMB/ECCB 2017 abstract submission
deadline is this Thursday 13 April - this is one of the biggest and
broadest commutational biology conferences and there will I'm sure be a
strong Galaxy presence.
I get two messages where I do not know how to continue:
The first seems to be severe:
tool_shed.util.common_util WARNING 2017-04-10 07:37:39,800 The URL
I've been trying to get a local galaxy running with an assortment of tools for
a local researcher. I'm a linux administrator rather than a bioinformatics
researcher and am familiar with how repo's work for RedHat, R and the like.
I've built tools for other groups at work and from my
I suspect the missing dependency BWA may reflect the switch away
from Galaxy's home-grown packaging system to using Conda -
enabled by default since v17.01,
Newer dependencies will likely next get an old fashioned package
I'm just starting to get jobs submitted to our cluster as real system
user. I read in the documentation that the name of the system user is
determined by "the Galaxy user's email address (with the @domain
stripped off)". But this does not work on our system, rather the
This may depend on the cluster setup, and how Galaxy accesses it.
What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup
usern...@example.org email aliases just for this.
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt wrote:
> Dear list,
sorry, I forgot this central piece of information: We also use Univa
What would be easier adapting galaxy's mapping to users or setting up
email aliases? I would need to ask our cluster admins if they could
On 10.04.2017 16:39, Peter Cock
That's interesting. I didn't set this up on our system, but if the LDAP can
tell Galaxy the real username, maybe we can avoid having to setup
usern...@example.org aliases and insisting our users do that for
logging into Galaxy.
Hopefully some other SGE users can comment on how they got the