README

Bio::ToolBox - Tools for querying and analysis of genomic data

DESCRIPTION

The Bio::ToolBox libraries provide a unified, abstracted interface 
to multiple common bioinformatic file formats, gene annotation 
(bed, gff, gtf, UCSC formats), and data storage formats (bam, bigWig, 
bigBed, USeq). Included are several high-quality end-user 
scripts for bioinformatic analysis, including working with gene 
annotation, collecting data scores from a variety of modern file 
formats relative to genomic annotation, and conversion between 
common file formats. 


REQUIREMENTS

These are Perl modules and scripts. They require Perl and a 
command-line environment. They have been developed and tested on Mac 
OS X and linux; Microsoft Windows compatability is not tested 
nor guaranteed.


INSTALLATION

Installation is simple with the Perl Module::Build incantation.

    perl ./Build.PL
    ./Build
    ./Build test
    ./Build install

Released versions may be obtained though the CPAN repository using 
your favorite package manager. 

Advanced installation notes are provided at
https://tjparnell.github.io/biotoolbox/AdvancedInstallation.html.


ADDITIONAL REQUIREMENTS

To make the installation as lean and simple as possible, only the minimal 
additional Perl modules are required, while the remainder are only 
recommended. These can be installed subsequently as necessary as the need 
arises. Most of the database adapters, including those for Bam, BigWig, 
and BigBed, require external library dependencies that must be compiled 
separately. See the respective modules for installation instructions.

Most scripts should fail gently with warnings about missing modules.


PROJECT WEBSITE

The BioToolBox project repository may be found at
https://github.com/tjparnell/biotoolbox. 

Full documentation, including common usage scenarios with the included
applications, may be found at https://tjparnell.github.io/biotoolbox.


LICENSE

This package is free software; you can redistribute it and/or modify
it under the terms of the Artistic License 2.0. For details, see the
full text of the license in the file LICENSE.

This package is distributed in the hope that it will be useful, but it
is provided “as is” and without any express or implied warranties. For
details, see the full text of the license in the file LICENSE.