Building Avocado from Source

You will need to have Apache Maven version 3.1.1 or later installed in order to build Avocado.

Note: The default configuration is for Hadoop 2.7.3. If building against a different version of Hadoop, please pass -Dhadoop.version=<HADOOP_VERSION> to the Maven command.

git clone https://github.com/bigdatagenomics/avocado.git
cd avocado
export MAVEN_OPTS="-Xmx512m -XX:MaxPermSize=128m"
mvn clean package -DskipTests

Outputs

...
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 9.647s
[INFO] Finished at: Thu May 23 15:50:42 PDT 2013
[INFO] Final Memory: 19M/81M
[INFO] ------------------------------------------------------------------------

You might want to take a peek at the scripts/jenkins-test script and give it a run. We use this script to test that Avocado is working correctly.

Running Avocado

Avocado is packaged as an überjar and includes all necessary dependencies, except for Apache Hadoop and Apache Spark.

You might want to add the following to your .bashrc to make running Avocado easier:

alias avocado-submit="${AVOCADO_HOME}/bin/avocado-submit"

$AVOCADO_HOME should be the path to where you have checked AVOCADO out on your local filesystem. The alias calls a script that wraps the spark-submit command to set up Avocado. You will need to have the Spark binaries on your system; prebuilt binaries can be downloaded from the Spark website. Our continuous integration setup builds ADAM against Spark 2.0.0, Scala versions 2.10 and 2.11, and Hadoop versions 2.3.0 and 2.6.0.

Once this alias is in place, you can run Avocado by simply typing avocado-submit at the command line.

avocado-submit