https://github.com/heuermh/biojava-legacy-adam

BioJava 1.x (biojava-legacy) and ADAM integration.
https://github.com/heuermh/biojava-legacy-adam

Last synced: 9 days ago
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BioJava 1.x (biojava-legacy) and ADAM integration.

• Host: GitHub
• URL: https://github.com/heuermh/biojava-legacy-adam
• Owner: heuermh
• License: lgpl-3.0
• Created: 2017-04-28T19:16:27.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2022-04-05T22:44:58.000Z (over 2 years ago)
• Last Synced: 2024-05-02T00:29:54.585Z (6 months ago)
• Language: Java
• Homepage:
• Size: 52.7 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: COPYING

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README

        
# biojava-legacy-adam

BioJava 1.x (biojava-legacy) and ADAM integration. 

### Hacking biojava-legacy-adam

Install

 * JDK 1.8 or later, http://openjdk.java.net

 * Apache Maven 3.8.5 or later, http://maven.apache.org

 * Apache Spark 3.2.0 or later, http://spark.apache.org

 * ADAM: Genomic Data System 0.37.0 or later, https://github.com/bigdatagenomics/adam

To build

    $ mvn install

To run

```

$ spark-shell \

    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \

    --conf spark.kryo.registrator=org.biojava.adam.BiojavaKryoRegistrator \

    --jars target/biojava-adam-legacy-$VERSION.jar,$PATH_TO_ADAM_ASSEMBLY_JAR

Welcome to

      ____              __

     / __/__  ___ _____/ /__

    _\ \/ _ \/ _ `/ __/  '_/

   /___/ .__/\_,_/_/ /_/\_\   version 3.2.0

      /_/

Using Scala version 2.12.15 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191)

Type in expressions to have them evaluated.

Type :help for more information.

scala> import org.biojava.adam.BiojavaAdamContext

import org.biojava.adam.BiojavaAdamContext

scala> val biojavaContext = new BiojavaAdamContext(sc)

biojavaContext: org.biojava.adam.BiojavaAdamContext = org.biojava.adam.BiojavaAdamContext@1e041848

```