Awesome

adam-commands

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

Hacking adam-commands

Install

• JDK 1.8 or later, http://openjdk.java.net
• Scala 2.12.15 or later, http://www.scala-lang.org
• Apache Maven 3.3.1 or later, http://maven.apache.org
• Apache Spark 3.2.1 or later, http://spark.apache.org
• ADAM: Genomic Data System 1.0 or later, https://github.com/bigdatagenomics/adam

To build

$ mvn install

Running adam-commands using adam-submit

$ cp target/adam-commands_2.12-${ADAM_VERSION}.jar $ADAM_DIR
$ cd $ADAM_DIR

To run the external commands in this repository via the ADAM command line, specify ADAM_MAIN and add the adam-commands jar to the classpath with the Spark --jars argument.

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

External commands are now listed in the usage text.

$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  --

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args:

       e        888~-_         e            e    e
      d8b       888   \       d8b          d8b  d8b
     /Y88b      888    |     /Y88b        d888bdY88b
    /  Y88b     888    |    /  Y88b      / Y88Y Y888b
   /____Y88b    888   /    /____Y88b    /   YY   Y888b
  /      Y88b   888_-~    /      Y88b  /          Y888b

Usage: adam-submit [<spark-args> --] <adam-args>

Choose one of the following commands:

ADAM ACTIONS
...

EXTERNAL COMMANDS
         count_alignments : Counts the alignments in a read dataset.
count_alignments_per_read : Counts the alignments per read in a read dataset.

Run external commands

$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  -- \
  count_alignments adam-core/src/test/resources/small.sam

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args: "count_alignments" "adam-core/src/test/resources/small.sam"
...
(1,20)


$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  -- \
  count_alignments_per_read adam-core/src/test/resources/small.sam

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args: "count_alignments_per_read" "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:1:5469106:true,1)
(simread:1:186794283:true,1)
(simread:1:189606653:true,1)
(simread:1:101556378:false,1)
(simread:1:37577445:false,1)
(simread:1:89554252:false,1)
(simread:1:153978724:false,1)
(simread:1:169801933:true,1)