SetupHadoopBAM

- Hadoop BAM:

git clone https://github.com/HadoopGenomics/Hadoop-BAM.git
version from POM: 7.7.1-SNAPSHOT
Modify POM.XML to include correct version of Hadoop on Cypress and pointer to
Hortonworks repository

export HADOOP_BAM="/home/lngo/git/Hadoop-BAM/"
hadoop version: 2.7.1.2.4.2.0-258
hortonworks repository:
<repository>
           <id>hortonworks</id>
           <url>http://repo.hortonworks.com/content/groups/public</url>
       </repository>

- Biodoop SEAL:
git clone https://github.com/crs4/seal.git

Module load anaconda/2.5.0
pip install --user pydoop
python setup.py build

- SeqPig:
git clone https://github.com/HadoopGenomics/SeqPig.git

Also edit pom to fix hadoop and hortonwork repository versions
Pig version: pig-0.15.0.2.4.2.0-258
use classifier to grab the h2 version, then change the name of the jar and .shal
file to math the required version listed in pom.xml


mvn install:install-file -Dfile=lib/seal.jar -DgroupId=it.crs4 -DartifactId=seal -Dversion=devel-bf3090f -Dpackaging=jar -DgeneratePom=true
mvn package -DskipTests

version is copied from the seal

export PIG_HOME="/usr/hdp/current/pig-client/"
export SEQPIG_HOME="/home/lngo/git/SeqPig"