Hi Iyad, does this part of our documentation help you?
https://github.com/bgruening/docker-galaxy-stable/tree/dev#using-an-external-slurm-cluster I now at least of one user that is using the Docker Image in a SLURM cluster environment. I don't see a reason why this should not work on SGE or condor as well. Ciao, Bjoern > Hi Everyone, > > 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 between the application server and cluster. > The galaxy wiki page refers to this as a "shared file system". I > suppose we can configure SGE to submit jobs as a specific user but > the resultant files would need to be chowned to the user within the > cluster and then back to the one inside the container. Is this > supported or has been tested? > > Regards, > > Iyad Kandalaft > > Acting Chief Bioinformatician in Biodiversity, STB Agriculture and > Agri-Food Canada / Government of Canada iyad.kandal...@agr.gc.ca / > Tel: 613-759-1228 / TTY: 613-773-2600 > > Bioinformaticien chef de la biodiversite interim, Direction générale > des Science et de la technologie Agriculture et Agroalimentaire > Canada / Gouvernement du Canada iyad.kandal...@agr.gc.ca / Tel: > 613-759-1228 / TTY: 613-773-2600 > > > > > -----Original Message----- From: galaxy-dev > [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of > Björn Grüning Sent: August-04-15 4:42 AM To: Tiago Rodrigues Antao; > Björn Grüning Cc: galaxy-...@lists.bx.psu.edu; Martin Page (TSL); > Oksana; Jeroen Galle Subject: Re: [galaxy-dev] Externalizing Galaxy > config in docker-galaxy-stable > > > > 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 quite a few tools. >> For example the RNA-Seq lacked tophat, cufflinks and cummrbund. I >> wanted to reuse as much as possible, but that was what made me >> stop. > > Create a PR! > https://github.com/bgruening/docker-recipes/blob/master/galaxy-rna-seq/Dockerfile > > >> I am currently using the stable one (docker-galaxy-stable) and >> advancing from there. But I would prefer to use a "stock" one. > > If you feel I can move this into it's own repository and out of > docker-recipes. PR welcome! HiSat should be also included I guess. > > I hope to make this flavours community driven, so I really > appreciate contributions to it. > > Ciao, Bjoern > >> Tiago >> > ___________________________________________________________ Please > keep all replies on the list by using "reply all" in your mail > client. To manage your subscriptions to this and other Galaxy lists, > please use the interface at: https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
