The directory structure created by the maven archetype includes a pom.xml file which is our Maven build file, a src directory which contains the Java workflow, and a workflow directory that contains any bundled data, the basic workflow config file which includes all the parameters this workflow accepts, the metadata.xml which defines the workflows available in this bundle, and any scripts, binaries, or libraries your workflow needs (in bin and lib respectively).
When you issue the mvn install command the
target directory is created
which contains the compiled workflow along with the various necessary files all
correctly assembled in the proper directory structure. You can
run the workflow in test mode or package up the workflow as a zip file for
exchange with others. Both topics are covered later in this tutorial.
The Maven archetype workflows are quite nice, too, since it is easy to check in everything but the target directory into source control like git or subversion. This makes it a lot easier to share the development of workflows between developers.
|-- pom.xml |-- src | `-- main | `-- java | `-- com | `-- github | `-- seqware | `-- MyHelloWorldWorkflow.java |-- target | `-- Workflow_Bundle_MyHelloWorld_1.0_SeqWare_1.1.0 | `-- Workflow_Bundle_MyHelloWorld | `-- 1.0 | |-- bin | |-- classes | | `-- com | | `-- github | | `-- seqware | | `-- MyHelloWorldWorkflow.class | |-- config | | `-- MyHelloWorldWorkflow.ini | |-- data | | `-- input.txt | |-- lib | | `-- seqware-distribution-1.1.0-full.jar | `-- metadata.xml |-- workflow | |-- config | | `-- MyHelloWorldWorkflow.ini | |-- data | | `-- input.txt | |-- lib | |-- metadata.xml | `-- workflows `-- workflow.properties
Here are some additional details about these files: