https://github.com/heuermh/adam-plugins

External plugins in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.
https://github.com/heuermh/adam-plugins

Last synced: 9 days ago
JSON representation

External plugins in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/heuermh/adam-plugins
• Owner: heuermh
• License: apache-2.0
• Created: 2014-03-12T22:04:26.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2016-07-06T22:02:25.000Z (over 8 years ago)
• Last Synced: 2024-05-02T00:29:37.846Z (6 months ago)
• Language: Java
• Homepage:
• Size: 84 KB
• Stars: 8
• Watchers: 3
• Forks: 4
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
adam-plugins

============

---

NOTE:  The ADAM plugin API was removed in https://github.com/bigdatagenomics/adam/pull/1065.

This project will no longer be updated.

---

External plugins in Java and Scala for ADAM: Genomic Data System.  Apache 2 licensed.

###Hacking adam-plugins

Install

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

 * Scala 2.10.5 or later, http://www.scala-lang.org

 * Apache Maven 3.2.5 or later, http://maven.apache.org

 * Apache Spark 1.6.1 or later, http://spark.apache.org

 * ADAM: Genomic Data System 0.19.1-SNAPSHOT or later, https://github.com/bigdatagenomics/adam

To build

    $ mvn install

### Running adam-plugins using ```adam-submit```

    $ cp target/adam-plugins_2.10-0.19.1-SNAPSHOT.jar $ADAM_DIR

    $ cd $ADAM_DIR

To run the plugins in this repository via the ADAM command line, add the jar to the classpath with the Spark ```--jars``` argument.

Note the ```--``` argument separator between Spark arguments and ADAM arguments.

Run plugins

    $ ./bin/adam-submit \

          --jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \

          -- \

          plugin com.github.heuermh.adam.plugins.CountAlignments \

          adam-core/src/test/resources/small.sam

     

    (1,20)

    $ ./bin/adam-submit \

          --jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \

          -- \

          plugin com.github.heuermh.adam.plugins.CountAlignmentsPerRead \

          adam-core/src/test/resources/small.sam

     

    (simread:1:237728409:true,1)

    (simread:1:195211965:false,1)

    (simread:1:163841413:false,1)

    (simread:1:231911906:false,1)

    (simread:1:26472783:false,1)

    (simread:1:165341382:true,1)

    (simread:1:240344442:true,1)

    (simread:1:50683371:false,1)

    (simread:1:240997787:true,1)

    (simread:1:14397233:false,1)

    (simread:1:207027738:true,1)

    (simread:1:20101800:true,1)

    (simread:1:101556378:false,1)

    (simread:1:37577445:false,1)

    (simread:1:189606653:true,1)

    (simread:1:5469106:true,1)

    (simread:1:186794283:true,1)

    (simread:1:89554252:false,1)

    (simread:1:153978724:false,1)

    (simread:1:169801933:true,1)