Best regards
Weiyan Shen‍‍

I think you want your job_conf.xml destination to have the parameter

<param id="docker_enabled">true</param>

not

<param id="smalt-galaxy">true</param>

Does this help any?

-John

On Thu, Nov 6, 2014 at 1:35 AM, Weiyan Shen <shenwiyn@gmail.com> wrote:
> 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
>
>
>
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