This package contains the Java and Scala bindings for the CIEL distributed execution engine. These bindings allow you to implement CIEL tasks using the Java and Scala programming langauges.
Before installing the CIEL Java bindings, you will need to install the Java Development Kit version 5.0 or later, and Apache Maven.
Once you have installed these prerequisites, you can build the bindings and examples by typing the following in the current directory:
$ mvn install
Next, copy the bindings to your JAR library folder. For example, using
$HOME/lib/ciel
:
$ mkdir -p $HOME/lib/ciel
$ cp bindings/target/*.jar $HOME/lib/ciel
$ cp scala-bindings/target/*.jar $HOME/lib/ciel # optional for Scala.
Also copy the GSON JAR from your Maven repository to your JAR library
folder. For example, if your Maven repository is in
~/.m2/repository
:
$ cp ~/.m2/repository/com/google/code/gson/gson/1.7.1/*.jar $HOME/lib/ciel
If you want to enable Scala support, also copy the Scala runtime library to your JAR library folder:
$ cp ~/.m2/repository/org/scala-lang/scala-library/2.8.1/scala-library-2.8.1.jar $HOME/lib/ciel
Finally, update your CIEL configuration with the location of your JAR library:
$ ciel config --set java.jar_lib $HOME/lib/ciel
The following command runs a simple test job, which prints "Hello, world!" on the terminal:
$ ciel java examples/target/ciel-examples-*.jar com.asgow.ciel.examples.HelloWorld
To run the Smith-Waterman example (on files named <PATH_TO_X>
and <PATH_TO_Y>
):
$ ciel java examples/target/ciel-examples-*.jar \
com.asgow.ciel.examples.smithwaterman.SmithWaterman \
<NUM_BLOCKS_X> <NUM_BLOCKS_Y> -P x=<PATH_TO_X> -P y=<PATH_TO_Y>