README

BioPig

BioPig Copyright (c) 2015, The Regents of the University of California, through Lawrence Berkeley National Laboratory 
(subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 
If you have questions about your rights to use or distribute this software, please contact 
Berkeley Lab's Technology Transfer Department at  TTD@lbl.gov referring to " BioPig (LBNL Ref CR-3209)."
 
NOTICE.  This software was developed under funding from the U.S. Department of Energy.  As such, the U.S. Government 
has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license 
in the Software to reproduce, prepare derivative works, and perform publicly and display publicly.  Beginning five (5)
 years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to 
 any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a 
 paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, 
 distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

This project provides additional apache pig commands and data loaders/writers specific
for biologicial sequence data.  Specifically, biopig supports the following functionality:
  - load fasta and fastq files
  - filter sequence data by id, header or size
  - generate kmers
  - wrappers for common external programs (Blast, Newbler, velvet, cap3, etc)

With biopig, users can write data parallel analysis tools that get executed on a hadoop
map/reduce cluster such as NERSC's Magellan or AWS's Elastic MapReduce.

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to build

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To build the software, you need to have maven.  install maven and then build using

   % mvn package -Dmaven.test.skip=true

this will produce a JAR file in biopig/target/biopig-<version>-all.jar


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to use

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see ./apps for examples.


questions/comments can be emailed to us at biopig [at] jgi-psf [dot] org