galaxyproject / galaxyproject/planemo

DNS not resolved inside container tool when using --mulled_containers

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#903 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

When starting planemo with with mulled containers support I get that tools which require DNS resolution (because for instance they need to download something) cannot resolve DNS addresses. If I run the same tool container manually through docker run, the container can resolve things fine. In both cases, the injected content on `/etc/resolve.conf` is the same. Maybe this is a wider Galaxy issue if the docker networking is being handled in any particular way by Galaxy

On `docker inspect` on the two cases, tool container sent by Galaxy and container run directly, I can see that the Galaxy one has `"NetworkMode": "none"` where as the working one has `"NetworkMode": "default"`. Is Galaxy on planemo actively setting this somehow?

Contributor guide

Open the contributing guide

Research direction

Start by reproducing the mulled-container case and comparing `docker inspect` output with the working `docker run` case, focusing on `NetworkMode` and `/etc/resolve.conf`. Trace the Planemo/Galaxy container-launch path to determine why the tool receives `NetworkMode: none`; done means the launched tool can resolve DNS as the manual container does.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
infrastructure, networking
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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