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