bigdatagenomics/cannoli

Name: cannoli

Owner: Big Data Genomics

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

Created: 2017-01-09 22:02:42.0

Updated: 2017-09-29 21:47:23.0

Pushed: 2017-11-08 22:18:27.0

Homepage: null

Size: 204

Language: Scala

GitHub Committers

User	Most Recent Commit	# Commits
Michael L Heuer	2018-03-22 16:42:26.0	59
Frank Austin Nothaft	2017-07-05 20:54:17.0	10
Walter Blair	2017-01-26 20:36:10.0	1

Other Committers

User	Email	Most Recent Commit	# Commits

README

cannoli

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

Hacking cannoli

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

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

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

se one of the following commands:

OLI
        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.

OLI 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