WIP (Work In Progress)
A LAPPS/Galaxy Docker Appliance, or simply an appliance, is a network of Docker containers running a Galaxy instance configured with a selected set of LAPPS Grid web services. Where the web services are also running in one or more other Docker containers. Typically services are organized into Docker containers by family, that is one container for StanfordNLP service, another container for Lingpipe, one for a MASC Datasource and Solr instance etc.
The make-appliance script expects the Tool Config Editor is installed and the tce script used to launch the editor is available on the $PATH. A pre-built binary distribution of the Tool Conf Editory is available here.
Groovy (2.4.x or later) is required to run the YamlBuilder.groovy script that is used to generate the docker-compose.yml file.
$> ./make-appliance identifier module [module ...]where the identifier is just a prefix for names of Docker containers, and a module is the name of the Docker containers to include in the appliance.
EXAMPLE
$> ./make-appliance gate masc oaqa
$> docker-compose upAssembling an appliance requires three things.
tool directory. Note: tools are not installed from Galaxy's Tool Shed since the tools used in an appliance do not make sense outside the context of the appliance. That is, other users would not be able to install the tools and use them so it does not make sense to deploy them to a tool shed.docker-compose.yml file needed to wire everything together.Some scripts and tools are provided to automate as much of the task as possible, but it is not too difficult to do everything by hand.
The web services running in the Docker containers should be SOAP services that support the LAPP Grid API. While not a hard requirement, it does make it easier to compose workflows in Galaxy if all service speak the same APIs and data formats. Implementing a LAPPS Grid service is beyond the scope of this document, but see this tutorial for information on writing a LAPPS Grid web service. The remainder of this document assumes the Service.war file containing a service named MyCustomService has already be created.
There are two ways to run a war file in a Docker container:
lappsgrid/tomcat7 image directly and mount the directory containing the Service.war file as /var/lib/tomcat7/webapps, orlappsgrid/tomcat7, or any other Tomcat7 based container.Create a new directory and copy the Service.war file. For this example it is assumed the Service.war file has been copied to /home/user/webapp, but any local directory will do. The use the -v option to mount this as a volume in the Docker image
$> docker run -d -p 8080:8080 -v /home/user/webapp:/var/lib/tomcat7/webappsAfter Docker has started the container the service can be accessed at http://localhost:8080/Service/services/MyCustomService.
Tomcat will expand and run all .war file it finds in /var/lib/tomcat7/webapps so if /home/user/webapp contains more than one .war file Tomcat will run them all.
Create a Dockerfile based on the lappsgrid/tomcat7 image and copy the war file to /var/lib/tomcat7/webapps.
FROM lappsgrid/tomcat7
COPY ./Service.war /var/lib/tomcat7/webappsSee here for more information on creating Docker images.
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