Hi John Chilton,
Thank you very much for your help. I changed my job_conf.xml as follow,it works!
<?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_volumes">$defaults</param>
<param id="docker_cmd">/usr/bin/docker</param>
<param id="docker_sudo">false</param>
<param id="docker_sudo_cmd">/usr/bin/sudo --extra_param</param>
<param
id="docker_container_id_override">smalt-galaxy:shenweiyan</param>
<param
id="dockers_default_container_id">smalt-galaxy:shenweiyan</param>
</destination>
</destinations>
</job_conf>
Best regards
Weiyan Shen
------------------ 原始邮件 ------------------
发件人: "John Chilton";<jmchil...@gmail.com>;
发送时间: 2014年11月6日(星期四) 晚上8:20
收件人: "Weiyan Shen"<shenw...@gmail.com>;
抄送: "galaxy-dev"<galaxy-dev@lists.bx.psu.edu>;
"galaxy-user"<galaxy-u...@lists.bx.psu.edu>;
主题: Re: [galaxy-dev] Integrating Docker-based tools within Galaxy failed
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 <shenw...@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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