Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.
Install
- JDK 1.8 or later, http://openjdk.java.net
- Apache Maven 3.3.9 or later, http://maven.apache.org
To build
$ mvn install
To run the commands in this repository via the ADAM command line, specify ADAM_MAIN and add the cannoli jar
to the classpath with the Spark --jars argument.
Note the -- argument separator between Spark arguments and ADAM arguments.
Cannoli commands are now listed in the usage text.
$ ADAM_MAIN=org.bdgenomics.cannoli.Cannoli \
adam-submit \
--jars cannoli_2.10-0.1-SNAPSHOT.jar \
--
Using ADAM_MAIN=org.bdgenomics.cannoli.Cannoli
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
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:
...
CANNOLI
bowtie : ADAM Pipe API wrapper for Bowtie.
bowtie2 : ADAM Pipe API wrapper for Bowtie2.
example : Example.
freebayes : ADAM Pipe API wrapper for Freebayes.
snpEff : ADAM Pipe API wrapper for SnpEff.