Hi;

I think I started a thread on a similar issue on this list. The answer was
to configure properly config/job_conf.xml, adding the docker runner and the
docker_net param within it to "bridge":

<?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>


Cheers

PS: my docker tool:
https://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy


2015-12-18 14:07 GMT+01:00 Bjoern Gruening <bjoern.gruen...@gmail.com>:

> 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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-- 
Mikel Egaña Aranguren, Ph.D.

http://mikeleganaaranguren.com
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