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 Cannoli command 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
bedtools : ADAM Pipe API wrapper for Bedtools intersect.
bowtie : ADAM Pipe API wrapper for Bowtie.
bowtie2 : ADAM Pipe API wrapper for Bowtie2.
bwa : ADAM Pipe API wrapper for BWA.
freebayes : ADAM Pipe API wrapper for Freebayes.
snpEff : ADAM Pipe API wrapper for SnpEff.
CANNOLI TOOLS
fastqInterleaver : Interleaves two FASTQ files
Command arguments follow the -- separator and command name.
$ ADAM_MAIN=org.bdgenomics.cannoli.Cannoli \
adam-submit \
--jars cannoli_2.10-0.1-SNAPSHOT.jar \
-- \
bwa --help
Using ADAM_MAIN=org.bdgenomics.cannoli.Cannoli
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INPUT : Location to pipe from, in interleaved FASTQ format.
OUTPUT : Location to pipe to.
SAMPLE : Sample ID.
-bwa_path VAL : Path to the BWA executable. Defaults to bwa.
-defer_merging : Defers merging single file output.
-docker_image VAL : Docker image to use.
Defaults to quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c.
-force_load_ifastq : Forces loading using interleaved FASTQ.
-force_load_parquet : Forces loading using Parquet.
-fragments : Saves OUTPUT as Fragments in Parquet. Exclusive of -single.
-h (-help, --help, -?) : Print help
-index VAL : Path to the bwa index to be searched, e.g. <ebwt> in bwa [options]* <ebwt> ...
-parquet_block_size N : Parquet block size (default = 128mb)
-parquet_compression_codec : Parquet compression codec
-parquet_disable_dictionary : Disable dictionary encoding
-parquet_logging_level VAL : Parquet logging level (default = severe)
-parquet_page_size N : Parquet page size (default = 1mb)
-print_metrics : Print metrics to the log on completion
-sequence_dictionary VAL : Path to the sequence dictionary.
-single : Saves OUTPUT as single file. Exclusive of -fragments.
-use_docker : If true, uses Docker to launch BWA. If false, uses the BWA executable path.