Problem adding/checking a docker tool

Question: Problem adding/checking a docker tool

6 days ago by

SamGG • 0

SamGG • 0 wrote:

Hi,

Newbie question.

I am following the installation of tool that is running within a docker container. I can run this tool on the command line of the Galaxy shell (the shell I use to run the Galaxy server). I followed the tuto at https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt. Neverthess the tool is not launching the docker environment.

Currently, I replaced the tool command by a simple "uname -a" command that returns a different result upon its environment. The result is the same as in the Galaxy server shell. I don't see any "docker run" in the log of the Galaxy server. I don't get any complain that Galaxy is not able to run or find docker command (but maybe I miss it). I didn't configure anything to tell Galaxy about docker.

Is there any very simple test that can make me confident that Galaxy could use/launch docker?

I will consider any advice. Sorry if I miss the answer to a similar question, but there are so many Q/A concerning the Galaxy docker image that could not find my way.

Best.

tool integration docker • 27 views

ADD COMMENT • link •

modified 5 days ago by Bjoern Gruening ♦ 5.1k • written 6 days ago by SamGG • 0

5 days ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi SamGG,

you need to configure Galaxy in a way that says ... run this tool preferably with Docker or Singularity or Conda or ... For example see the advanced example job_conf file: https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L376

Hope that gets you started, Bjoern

ADD COMMENT • link written 5 days ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern, Thanks for your answer. I didn't configure that part of Galaxy yet. What are the risks (mainly security) of running directly the docker command from the script section of the XML? Best, Samuel

ADD REPLY • link written 4 days ago by SamGG • 0

I don't know. No others than the usual Docker risks I think. But Galaxy has a better control over the data flow, so I would avoid running it from the commandline. This also seems to be non-portal to other Galaxy instances. So ideally a Galaxy tool should just describe the tool and don't do any assumptions about the runtime environment. This should be done by Galaxy and the Galaxy admin.

ADD REPLY • link written 4 days ago by Bjoern Gruening ♦ 5.1k

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