Hi,
I have a couple of GATK issues
1. First is there a data manager for it? I have tried Generate
GATK-sorted Picard indexes (data_manager_gatk_picard_index_builder) -
builder and got no entries on the cached picard genomes.
2. With problem 1, we are using genomes from the history. It so happens
On Tue, 20 Oct 2015 14:48:08 +0200
Bjoern Gruening wrote:
> Hi Tiago,
>
> for simple tool_dependencies you can use the new planemo depbash
> command from Peter:
> https://github.com/galaxyproject/planemo/pull/310
Gosh, this is exactly what the doctor ordered. Thanks (to Peter also).
> What k
Hi,
I am afraid that I might be overlooking something obvious but...
I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For
that effect I am designing a few package wrappers. My problem is to
understand the best practice to develop wrappers for dependencies of
external tools.
For
On Thu, 06 Aug 2015 14:00:02 +0200
Björn Grüning wrote:
> 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.
>
> B
On Wed, 5 Aug 2015 14:10:57 -0500
Eric Rasche wrote:
>- http://wookoouk.github.io/galaxyFlavorGenerator/
>- https://github.com/galaxyFlavorsGenerators/galaxyFlavorGenerator/
The first link works (for Docker), but the second has only a (empty)
readme file...
_
On Tue, 4 Aug 2015 17:26:00 +
"Kandalaft, Iyad" 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 path and UID/GID betw
On Mon, 03 Aug 2015 17:30:05 +0200
Björn Grüning 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, cufflinks and cummrbund. I
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 i
