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 command line, use cannoli-submit.
Note the -- argument separator between Spark arguments and Cannoli command arguments.
$ ./bin/cannoli-submit --help
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Usage: cannoli-submit [<spark-args> --] <cannoli-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
interleaveFastq : Interleaves two FASTQ files.
sampleReads : Sample reads from interleaved FASTQ format.
External commands wrapped by Cannoli should be installed to each executor node in the cluster
$ ./bin/cannoli-submit \
<spark-args>
-- \
bwa \
sample.unaligned.fragments.adam \
sample.bwa.hg38.alignments.adam \
sample \
-index hg38.fa \
-sequence_dictionary hg38.dict \
-fragments \
-add_indices
or can be run using Docker.
$ ./bin/cannoli-submit \
<spark-args>
-- \
bwa \
sample.unaligned.fragments.adam \
sample.bwa.hg38.alignments.adam \
sample \
-index hg38.fa \
-sequence_dictionary hg38.dict \
-fragments \
-use_docker \
-docker_image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
-add_indices