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Modules for community biology
Latest commit 67d0554 fangly Better use relative epsilon comparisons in Rarefier due to the large … …
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 Moose::Util::TypeConstraints MooseX::NonMoose MooseX::StrictConstructor PerlIO:eol Scalar::Util Tie::IxHash Test::Number::Delta This other module is recommended: Math::GSL::SF 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: firstname.lastname@example.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 <email@example.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.