Add README in rst format for PyPi

Modify setup files as needed

README.md

@@ -44,7 +44,7 @@ Each tool in the BuddySuite has been extensively documented in the [wiki](https:
 * [SeqBuddy](https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy) 
 * [AlignBuddy](https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy)
 * [PhyloBuddy](https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy)
-* [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy). 
+* [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy)
 
 ## Developers
 All of the individual Buddy toolkits are located in the 'buddysuite' directory and the 

README.rst

@@ -0,0 +1,89 @@
+|Build Status| |Coverage Status| |PyPi version|
+
+|BuddySuite|
+
+--------------
+
+Description
+-----------
+
+The BuddySuite modules are 'one-stop-shop' command line tools for common
+biological data file manipulations. Formats are detected automatically,
+conversions are seamless, and you can pipe into or out of the modules,
+allowing you to spend more time analyzing your sequences, alignments,
+and phylogenetic trees, instead of wrangling them.
+
+For example, the following command reads in three sequence files (all in
+different formats), pulls out records with RefSeq identifiers, calls
+MAFFT to generate an alignment, shifts gaps to force a codon alignment,
+calls RAxML to infer a phylogeny, and then roots the tree at its
+midpoint.
+
+``$: seqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records "[XN]M" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root``
+
+BuddySuite is a Python3 project, developed and extensively tested on
+Linux and Mac OS X. Full release versions are also tested on Windows
+before release, so should work as expected on Vista and above.
+
+Getting started
+---------------
+
+The simplest way to get up and running is:
+
+.. code:: bash
+
+    $: pip install buddysuite
+    $: buddysuite -setup
+
+Further instructions are available in the `installation
+guide <https://github.com/biologyguy/BuddySuite/wiki/Installation-Guide>`__.
+
+There is also a short `Beginners'
+Guide <https://github.com/biologyguy/BuddySuite/wiki/Beginners-Guide>`__
+to show you the basics.
+
+Each tool in the BuddySuite has been extensively documented in the
+`wiki <https://github.com/biologyguy/BuddySuite/wiki>`__, complete with
+worked examples and explanations for all arguments/options.
+
+-  `SeqBuddy <https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy>`__
+-  `AlignBuddy <https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy>`__
+-  `PhyloBuddy <https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy>`__
+-  `DatabaseBuddy <https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy>`__
+
+Developers
+----------
+
+All of the individual Buddy toolkits are located in the 'buddysuite'
+directory and the `'develop'
+branch <https://github.com/biologyguy/BuddySuite/tree/develop>`__ is
+where all new features have been implemented. If you're interested in
+contributing, please refer to the `developer
+page <https://github.com/biologyguy/BuddySuite/wiki/Developers>`__ for
+further information on dependencies and instructions.
+
+Citation
+--------
+
+We are currently working on a `peer reviewed
+manuscript <https://github.com/biologyguy/BuddySuite/tree/develop/manuscript>`__,
+but until then there is a very short application note on bioRxiv that
+can be cited if you use BuddySuite in your work.
+
+`DOI: 10.1101/040675 <http://dx.doi.org/10.1101/040675>`__
+
+Contact
+-------
+
+Any comments you have would be really appreciated. Please feel free to
+add issues in the GitHub issue tracker or contact Steve Bond (lead
+developer) directly at steve.bond@nih.gov.
+
+.. |Build Status| image:: https://travis-ci.org/biologyguy/BuddySuite.svg?branch=master
+   :target: https://travis-ci.org/biologyguy/BuddySuite
+.. |Coverage Status| image:: https://coveralls.io/repos/github/biologyguy/BuddySuite/badge.svg?branch=master
+   :target: https://coveralls.io/github/biologyguy/BuddySuite?branch=master
+.. |PyPi version| image:: https://img.shields.io/pypi/v/buddysuite.svg
+   :target: https://pypi.python.org/pypi/buddysuite
+.. |BuddySuite| image:: https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/BuddySuite-logo.gif
+   :target: https://github.com/biologyguy/BuddySuite/wiki

setup.cfg

@@ -1,2 +1,2 @@
 [metadata]
-description-file = README.md
+description-file = README.rst

setup.py

@@ -75,10 +75,10 @@ def run():
 }
 
 setup(name='buddysuite',
-      version='1.2b.3',
+      version='1.2b.6',
       description='BuddySuite is a collection of command line utilities written in Python for '
                   'working with biological data.',
-      long_description=open(os.path.join(os.path.dirname(__file__), 'README.md'), encoding="utf-8").read(),
+      long_description=open(os.path.join(os.path.dirname(__file__), 'README.rst'), encoding="utf-8").read(),
       author='Stephen Bond',
       author_email='steve.bond@gmail.com',
       url='https://github.com/biologyguy/BuddySuite',