Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

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,

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

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

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

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

[galaxy-dev] Developing package wrappers

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.

Re: [galaxy-dev] Developing package wrappers

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

[galaxy-dev] GATK issues

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