Question: Integrating Docker-based tools within Galaxy failed
0
gravatar for shenwiyn
3.5 years ago by
shenwiyn0
shenwiyn0 wrote:

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!

docker • 1.2k views
ADD COMMENTlink modified 3.3 years ago by jmchilton1.0k • written 3.5 years ago by shenwiyn0
0
gravatar for jmchilton
3.3 years ago by
jmchilton1.0k
United States
jmchilton1.0k wrote:

I believe this was followed up with a galaxy-dev post here https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-November/020892.html.

ADD COMMENTlink written 3.3 years ago by jmchilton1.0k
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