Integrating Docker-based tools within Galaxy failed

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Integrating Docker-based tools within Galaxy failed

shenwiyn
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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Re: Integrating Docker-based tools within Galaxy failed

John Chilton-4
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 <[hidden email]> 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
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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回复: Integrating Docker-based tools within Galaxy failed

shenwiyn

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";<[hidden email]>;
发送时间: 2014年11月6日(星期四) 晚上8:20
收件人: "Weiyan Shen"<[hidden email]>;
抄送: "galaxy-dev"<[hidden email]>; "galaxy-user"<[hidden email]>;
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 <[hidden email]> 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
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/