<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="docker_local">
<destination id="local" runner="local"/>
<destination id="docker_local" runner="local">
<param id="docker_enabled">true</param>
<param id="docker_memory">6G</param>
<param id="docker_sudo">false</param>
<param id="docker_net">bridge</param>
</destination>
</destinations>
</job_conf>Hi Jocelyn,
are you referring to the Docker --net option?
https://docs.docker.com/engine/userguide/networking/dockernetworks/
If so you can change the --net option during container startup. For example with
docker run --net=host -p 8080:80 bgruening/galaxy-stable
I'm wondering if there is not an other issue in your configuration because Galaxy in Docker can connect to the internet without problems.
Indeed all our flavours rely on the fact that you can install tools from the ToolShed.
Docker containers can have problems with pause and resume on Notebooks, so maybe a restart of your container fixes it?
Thanks for using Galaxy!
Bjoern
On 18.12.2015 13:59, Brayet Jocelyn wrote:
Dear Galaxy team,
I'm Jocelyn Brayet, I’m a bioinformatician of Institut Curie (France). I work with Alban Lermine on Galaxy tools development.
I currently create tools in Docker for the Galaxy Tool Shed. But, when Galaxy runs Docker, it adds the "—net None" option.
The issue is that my tools require annotation files that are downloaded when the job is running (only if the annotation file is not yet available).
With "—net None" option I cannot download these annotation files in a Docker.
I would like to know if there is a way to switch off this "--net None" option, for instance through the galaxy.ini file ?
If so, the user would have the choice to allow Docker to download these files.
Many thanks for your feedbacks
Best regards
Jocelyn
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