Hi,
I integrated Docker-based tools SMALT whin my local Galaxy by the guid:https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt, I found my Galaxy failed to integrate with my docker.

My docker images:
=> docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
smalt-galaxy        shenweiyan          bae67dfe69b5        2 hours ago         401.9 MB
ubuntu              14.04               5506de2b643b        12 days ago         197.8 MB
fedora              latest              7d3f07f8de5f        4 weeks ago         374.1 MB

My job_conf.xml:
=> cat job_conf.xml
<?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="smalt-galaxy">true</param>
          </destination>
    </destinations>
</job_conf>

SMALT can run successfuly by the command line:
$ docker run -v /App/Docker/smalt:/App/Docker/smalt:rw -w /App/Docker/smalt -i -t smalt-galaxy:shenweiyan smalt_wrapper.py -r /App/Docker/smalt/reference -f /App/Docker/smalt/reads.fastq -u /App/Docker/smalt/smalt.out

The SMALT in my Galaxy seems to work with my local samlt_x86_64 only,rather than in my smalt-galaxy image .
Could you give me some advices on how to solve these problems? Thanks very much!


Best regards
Weiyan Shen