{"id":17955544,"url":"https://github.com/heuermh/adam-plugins","last_synced_at":"2025-03-25T01:31:26.975Z","repository":{"id":14960942,"uuid":"17685737","full_name":"heuermh/adam-plugins","owner":"heuermh","description":"External plugins in Java and Scala for ADAM: Genomic Data System. 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Apache 2 licensed.\n\n\n###Hacking adam-plugins\n\nInstall\n\n * JDK 1.8 or later, http://openjdk.java.net\n * Scala 2.10.5 or later, http://www.scala-lang.org\n * Apache Maven 3.2.5 or later, http://maven.apache.org\n * Apache Spark 1.6.1 or later, http://spark.apache.org\n * ADAM: Genomic Data System 0.19.1-SNAPSHOT or later, https://github.com/bigdatagenomics/adam\n\n\nTo build\n\n    $ mvn install\n\n\n### Running adam-plugins using ```adam-submit```\n\n    $ cp target/adam-plugins_2.10-0.19.1-SNAPSHOT.jar $ADAM_DIR\n    $ cd $ADAM_DIR\n\n\nTo run the plugins in this repository via the ADAM command line, add the jar to the classpath with the Spark ```--jars``` argument.\n\nNote the ```--``` argument separator between Spark arguments and ADAM arguments.\n\nRun plugins\n\n    $ ./bin/adam-submit \\\n          --jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \\\n          -- \\\n          plugin com.github.heuermh.adam.plugins.CountAlignments \\\n          adam-core/src/test/resources/small.sam\n     \n    (1,20)\n\n\n    $ ./bin/adam-submit \\\n          --jars adam-plugins_2.10-0.19.1-SNAPSHOT.jar \\\n          -- \\\n          plugin com.github.heuermh.adam.plugins.CountAlignmentsPerRead \\\n          adam-core/src/test/resources/small.sam\n     \n    (simread:1:237728409:true,1)\n    (simread:1:195211965:false,1)\n    (simread:1:163841413:false,1)\n    (simread:1:231911906:false,1)\n    (simread:1:26472783:false,1)\n    (simread:1:165341382:true,1)\n    (simread:1:240344442:true,1)\n    (simread:1:50683371:false,1)\n    (simread:1:240997787:true,1)\n    (simread:1:14397233:false,1)\n    (simread:1:207027738:true,1)\n    (simread:1:20101800:true,1)\n    (simread:1:101556378:false,1)\n    (simread:1:37577445:false,1)\n    (simread:1:189606653:true,1)\n    (simread:1:5469106:true,1)\n    (simread:1:186794283:true,1)\n    (simread:1:89554252:false,1)\n    (simread:1:153978724:false,1)\n    (simread:1:169801933:true,1)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fadam-plugins","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fheuermh%2Fadam-plugins","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fheuermh%2Fadam-plugins/lists"}