BioR pipeline toolkit (main project)
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BioinformaticsToolsAtMayo/bior_pipeline
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= Building = You can build the project by running using the following different methods: 1. COMMAND LINE: mvn clean package 2. M2ECLIPSE: Right-click and select Run As --> Maven Build... Under Goals enter "clean package" Click Run The maven build produces the build artifacts under the ${project}/target folder. = Setup = Prior to running any project executables, the following must be setup: 1. Setup your UNIX environment: 1.1 open terminal 1.2 cd ${project} 1.3 mvn clean package # runs the build to create the distribution 1.4 source setupEnv.sh # inspects the target folder to setup env vars = Running = Execute any of the CLI scripts from your shell. Since all scripts are prefixed with "bior" by convention, TAB'ing after typing "bior" will show you all of the CLI commands. = Functional Tests = These are implemented as JUnit test cases executed by the maven-failsafe-plugin http://maven.apache.org/surefire/maven-failsafe-plugin that is designed to run functional/integration tests. The plugin finds the correct JUnit test cases via the classname suffix "ITCase". To execute the functional tests, you need to run the maven build w/ the "verify" phase: 1. COMMAND LINE: mvn clean verify 2. M2ECLIPSE: Right-click and select Run As --> Maven Build... Under Goals enter "clean verify" Click Run
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