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genomicwarehouse's Introduction

GenomicWarehouse Build Status

This is an open source project that attempts to answer important genomics questions on the big data platform

High Level Goals

  1. Recalculate
  2. Ingest
  3. Export
  4. Filter
  5. Interaction

Setup requirements

  • Essentials
    • Be able to scale cluster up and down as needed
    • Hortonworks Data Platform v2.3.4 installed on Azure
    • Install Java v8
    • HDFS
    • Spark
    • HBase
    • Create infrastructure for evaluation
      1. local sandbox for testing / development
      2. "small cluster", 3x 8C/32G/10T+
      3. "medium cluster", 5x 8C/32G/10T+
      4. "large cluster", 7x 8C/32G/10T+
  • Optional, but nice to have
    • Jypter
    • Zepplin

Plan

Building

This project uses Maven as a build system. Maven is an old standby build system for Java. It may be downloaded here, or installed via MacPorts, e.g. sudo port install maven. GenomicWarehouse is build on Java 1.8 or higher.

For Maven noobs beginners, there is a nice getting started guide.

To build the hadoop-commons code:

mvn compile

To run the set of unit tests:

mvn test

To include the (longer) integration tests:

mvn failsafe:integration-test

Getting Maven to fetch source and javadoc is easy:

mvn dependency:sources
mvn dependency:resolve -Dclassifier=javadoc

Dependancies

To add a dependency, edit the pom.xml file, looking for the <dependancies> section, e.g.

        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-core_2.10</artifactId>
            <version>1.5.2</version>
        </dependency>

Should be mostly self-explanatory.

Deployment

To deploy the CLI, build a jar file with an embedded classpath. This is done through this Maven plugin:

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-jar-plugin</artifactId>
    <configuration>
    <archive>
        <manifest>
        <addClasspath>true</addClasspath>
        <classpathPrefix>lib/</classpathPrefix>
        <mainClass>edu.mayo.genomics.LoadVCF</mainClass>
        </manifest>
    </archive>
    </configuration>
</plugin>

Maven can also collect the library jar files into target/lib:

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-dependency-plugin</artifactId>
    <version>2.5.1</version>
    <executions>
      <execution>
        <id>copy-dependencies</id>
        <phase>package</phase>
        <goals>
        <goal>copy-dependencies</goal>
        </goals>
        <configuration>
        <outputDirectory>${project.build.directory}/lib/</outputDirectory>
        </configuration>
      </execution>
    </executions>
</plugin>            

Install on cluster:

rsync -r --progress target/warehouse-1.0-SNAPSHOT.jar target/lib cluster:path/

genomicwarehouse's People

Contributors

blezek avatar david-w-mead avatar drachimera avatar romanzenka avatar

Watchers

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