I believe this is the result of a Docker bug
https://github.com/docker/docker/issues/7792 - (tl;dr a change in go
resulted in the volume map being randomized). This bug and supporting
Docker volume handling pre, during, and post bug is going to be
complicated and I need to work out if that is even possible. So there
are some workarounds:

 - Move your job working directory and files_path outside of galaxy_root.

(or)

 - Mount everything beneath GALAXY_ROOT read-write instead of mixing
read-only and read-write. Basically add the following to your job
destination:

<param 
id="docker_volumes">$galaxy_root:rw,$tool_directory:rw,$working_directory:rw,$default_file_path:rw</param>

This is second option is less secure of course - but no less secure
than not running things inside of the docker container. For strong
security inside of Docker I recommend using Pulsar.

Hope this helps,
-John


On Fri, Nov 14, 2014 at 12:55 AM, Weiyan Shen <shenw...@gmail.com> wrote:
> Dear all ,
> I am following the guide on
> https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt‍ to test
> the smalt docker integration tutorial.
>
> The SMALT within docker on my local Galaxy sometimes works well as follow:
>
> 502       7789  0.0  0.0 271680  6236 ?        Sl   21:42   0:00
> /usr/bin/docker run -e GALAXY_SLOTS=1 -v
> /data/Docker/galaxy-dist:/data/Docker/galaxy-dist:ro -v
> /data/Docker/galaxy-dist/tools/docker:/data/Docker/galaxy-dist/tools/docker:ro
> -v
> /data/Docker/galaxy-dist/database/job_working_directory/000/82:/data/Docker/galaxy-dist/database/job_working_directory/000/82:rw
> -v
> /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw
> -v
> /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw
> -w /data/Docker/galaxy-dist/database/job_working_directory/000/82 --net none
> smalt-galaxy:shenweiyan
> /data/Docker/galaxy-dist/database/job_working_directory/000/82/container.sh
>
> But sometimes it failed with the error:
>
> setup mount namespace bind mounts Creating new bind-mount target, mkdir
> /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files::
> read-only file system2014/11/14 21:28:13 Error response from daemon: Cannot
> start container
> 405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b: setup
> mount namespace bind mounts Creating new bind-mount target, mkdir
> /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files::
> read-only file system‍
>
> ‍‍It seems that docker running with sudoer unsteadily.Any idear how do I fix
> it?
>
>
> Kind regards,
> weiyan‍
>
>
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