Hi,
the first one is the one we are currently working on. It's an interface
to create your own Galaxy Docker flavours. Drag Drop your tools data
managers and so on ... click build and either get a Docker Image or a
Docker file.
But everything is in flux at the moment. So please jump in and
Hi Brian, Oksana,
let's move this discussion to github and try to get something done for
the next+1 release.
15.07/15.08 or what ever it will be is really close so I would like to
not rush here. But as soon as we have release this version. We can try
to get something in :dev that addresses these
Thanks!
@Brian please add your ideas and use cases so we can figure out a way
how to support this :)
Thanks,
Bjoern
Am 05.08.2015 um 16:26 schrieb Oksana Korol:
Created issue #74, with reference to this discussion.
Cheers,
Oksana
On Wed, Aug 5, 2015 at 9:52 AM, Björn Grüning
On Tue, 4 Aug 2015 17:26:00 +
Kandalaft, Iyad iyad.kandal...@agr.gc.ca wrote:
As a supplement to Oksana's original inquiry, we, at AAFC, couple
Galaxy to SGE and possibly a different grid engine in the future for
job scheduling. The old-fashioned way of doing that is to unify
storage
Tiago,
Some work is already in progress for that. Please see
- http://wookoouk.github.io/galaxyFlavorGenerator/
- https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/
I don't believe it handles configuration of the cluster backend, but I'm
sure that would be a good addition
Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao:
On Mon, 03 Aug 2015 17:30:05 +0200
Björn Grüning bjoern.gruen...@gmail.com wrote:
I would recommend you Galaxy Flavours. We have a few, for example
RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked
On Sun, Aug 2, 2015 at 4:59 AM, Oksana oko...@gmail.com wrote:
We only have one cluster, so we will have both test and production
environments running on it. I understand that at a minimum we'd need
different Galaxy home dir and UID/GID.
For our local deployment of Galaxy with Docker, which
On Mon, 03 Aug 2015 17:30:05 +0200
Björn Grüning bjoern.gruen...@gmail.com wrote:
I would recommend you Galaxy Flavours. We have a few, for example
RNA-Seq, ChIP-seq etc ... join us! :)
That was my first port of call, but they lacked quite a few tools. For
example the RNA-Seq lacked tophat,
Hi,
I am also thinking in doing something similar.
My idea would be to deploy a galaxy docker on demand per project. The
docker would have a galaxy installation that would be configured to
join a cluster. Most of the computation would actually occur on the
cluster.
Each project would thus have
Hi,
I will think about this, but this comes with the price of doing much of
the internal stuff during startup, which also have it's downsides.
Can you tell me what your admin wants to do, maybe we find a solution
without changing the build-time variables?
For example we can talk to schedulers
We only have one cluster, so we will have both test and production environments
running on it. I understand that at a minimum we'd need different Galaxy home
dir and UID/GID. This is a proof of concept for us still, so I can't tell you
what else we might need to change. I can get hold of our
Hi Oksana,
both variables are used during container build to create users and home
directories. This does not happen during container startup. They are
buildtime variables.
All Galaxy ENV vars are runtime variables and do have an impact during
startup.
Can you tell us more about what you want
Hi Bjorn,
Our team is trying to streamline our Galaxy development process, by using your
docker container for development, test and production environments. To do that,
our sys admin needs to be able to change a few of Galaxy build time variables,
like the ones that I've mentioned and probably
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