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";jmchilton@gmail.com; 发送时间: 2014年11月6日(星期四) 晚上8:20 收件人: "Weiyan Shen"shenwiyn@gmail.com; 抄送: "galaxy-dev"galaxy-dev@lists.bx.psu.edu; "galaxy-user"galaxy-user@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 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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