Bio-Community
==========================


ABOUT

The Bio-Community distribution contains a set of generic, open, object-oriented,
cross-platform Perl modules to represent and manipulate communities of
biological organisms. Bio-Community is part of the BioPerl project
(http://bioperl.org/).


INSTALLATION & DEPENDENCIES

Bio-Community requires Perl 5.10 or above. Additionally, these Perl modules are
required and will be installed during the installation procedure:

  BioPerl version >= 1.6.923
  DateTime
  Getopt::Euclid
  JSON::XS
  Hash::Util
  Math::Random::MT
  Method::Signatures
  Module::Runtime
  Moose
  MooseX::NonMoose
  MooseX::StrictConstructor
  PerlIO:eol
  Scalar::Util
  Tie::IxHash
  Test::Number::Delta

These other modules are recommended:
  Math::GSL::SF
  Math::GSL::Randist
  Math::GSL::RNG

The easiest way to install Bio-Community is using the CPAN way. See the detailed
instructions at http://www.cpan.org/modules/INSTALL.html

To install the Bio-Community modules by hand, type the following in a terminal:
   perl Build.PL
   ./Build installdeps   (as administrator)
   ./Build
   ./Build test
   ./Build install       (as administrator)


OVERVIEW

The ./lib/ folder contains the Bio-Community modules, which provide various
objects and operations:

 * The main objects are the community, member and metacommunity, provided by
   Bio::Community, Bio::Community::Member and Bio::Community::Meta, respectively

 * Reading and writing files in various formats, e.g. QIIME, biom, is possible
   through Bio::Community::IO

 * Alpha, beta and gamma diversity metrics are implemented in the modules
   Bio::Community::Alpha, Bio::Community::Meta::Beta and Bio::Community::Meta::Gamma

 * Bio::Community::Tools::* are modules providing various operations like random
   sampling, rarefaction or taxonomic summaries.

The ./scripts/ folder contains scripts. All these scripts use the Bio::Community
modules and are useful for reading or writing files, rarefying, 
They are good examples of how Bio::Community modules can be used as building
blocks for more complex programs. For convenience, all scripts are prefixed with
'bc_'.

The ./t/ folder contains unit tests to ensure the proper functioning of the
Bio-Community mocules. The ./t/data/ further contains data files used for the
tests and is thus a good source of example data.


BUGS, SUPPORT AND CONTRIBUTIONS

User feedback is an integral part of the evolution of these BioPerl modules.
Please direct usage questions or support issues to the mailing list, rather
than to the module maintainer directly:
   bioperl-l@bioperl.org
Many experienced and reponsive experts will be able look at the problem and
quickly address it. Please include a thorough description of the problem with
code and data examples if at all possible.

If you have found a bug, please report it on the BioPerl bug tracking system
to help us keep track the bugs and their resolution:
   https://redmine.open-bio.org/projects/bioperl/

The development code for Bio-Community is hosted on GitHub. To fork it and
start hacking, simply run:
   git clone https://github.com/bioperl/Bio-Community.git


COPYRIGHT

Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.

