Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
assembly
bin
cli
core
distribution
images
scripts
.gitignore
CHANGES.md
CODE_OF_CONDUCT.md
KEYS
LICENSE.txt
LICENSE_header.txt
README.md
pom.xml

README.md

cannoli

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

Build Status Maven Central API Documentation

cannoli project logo

Hacking cannoli

Install

To build

$ mvn install

Running cannoli

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

                              _ _ 
                             | (_)
   ___ __ _ _ __  _ __   ___ | |_ 
  / __/ _` | '_ \| '_ \ / _ \| | |
 | (_| (_| | | | | | | | (_) | | |
  \___\__,_|_| |_|_| |_|\___/|_|_|

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

Choose one of the following commands:

CANNOLI
        bcftoolsNorm : ADAM Pipe API wrapper for BCFtools norm.
   bedtoolsIntersect : ADAM Pipe API wrapper for Bedtools intersect.
              bowtie : ADAM Pipe API wrapper for Bowtie.
             bowtie2 : ADAM Pipe API wrapper for Bowtie 2.
                 bwa : ADAM Pipe API wrapper for BWA.
           freebayes : ADAM Pipe API wrapper for Freebayes.
     samtoolsMpileup : ADAM Pipe API wrapper for samtools mpileup.
              snpEff : ADAM Pipe API wrapper for SnpEff.
         vtNormalize : ADAM Pipe API wrapper for vt normalize.

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 \
    -image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
    -add_indices

or can be run using Singularity

$ ./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_singularity \
    -image quay.io/ucsc_cgl/bwa:0.7.12--256539928ea162949d8a65ca5c79a72ef557ce7c \
    -add_indices