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 > > > > ___________________________________________________________ > 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/