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!
