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Question: Galaxy + Condor + Docker
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gravatar for xiao2
2.5 years ago by
xiao2 • 10
xiao2 • 10 wrote:

Hello,

We know Galaxy support Docker, but it seems I can only run docker containers locally. Condor now has a Docker universe, which can manage docker jobs in a compute node. Is it possible to launch Galaxy's Docker jobs into condor?

Or is there a better way to launch Docker jobs to compute nodes in Galaxy?

Thanks in advance, Mark
galaxy • 1.3k views
ADD COMMENT • link •
modified 2.5 years ago by Bjoern Gruening ♦ 5.1k • written 2.5 years ago by xiao2 • 10
2
gravatar for Bjoern Gruening
2.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Mark,

in the latest development version of Galaxy has support for HTCondor and the Docker-universe. But we still need real world testers :) Have a look at this PR: https://github.com/galaxyproject/galaxy/pull/2278

Recently the Galaxy team also merged a PR which integrates a Kubernetes job runner, see here: https://github.com/galaxyproject/galaxy/pull/2314

So you have these two options. Docker Swarm I would not recommend it is currently not secure and please keep in mind this is all in Galaxy dev and will be released with Galaxy 16.07. I would really like to see some testing before so please get in touch with us if you find problems.

In a related new we also have merged HTCondor Integration into the Galaxy-Docker Image here: https://github.com/bgruening/docker-galaxy-stable/pull/180

So it should be possible to run Galaxy in Docker and submit via HTCondor Docker containers ;)

Ciao, Bjoern
ADD COMMENT • link written 2.5 years ago by Bjoern Gruening ♦ 5.1k
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