Merge pull request #23 from druvus/master

Update documentation

INSTALL.md

@@ -4,7 +4,25 @@ dependencies listed below. The software is developed and tested with Python
 version 2.7 but earlier (2.5, 2.6) may work just as well. Due to other 
 dependencies other versions of Python are not supported.
 
-To install CanSNPer, start by cloning this repo, change into the CanSNPer directory and
+### Bioconda
+With an activated Bioconda channel (see [Set up channels](https://bioconda.github.io/index.html#set-up-channels)), 
+install with:
+`conda install cansnper`
+and update with:
+`conda update cansnper`
+
+This will install CanSNPer with all Python and other dependencies (except progressivemauve).
+
+Remark that Bioconda only supports MacOS and Linux systems. 
+
+### Python Package Index
+An alternative way to install CanSNPer and Python dependencies is using PyPI with: 
+`pip install cansnper`
+
+Non-Python dependencies needs to be installed manuelly. See dependency secion below.
+
+### Latest source code
+To install the latest source code, start by cloning this repo, change into the CanSNPer directory and
 run the setup file. This will install CanSNPer and the Python dependecies.
 
 ```
@@ -13,6 +31,9 @@ cd CanSNPer
 python setup.py
 ```
 
+Non-Python dependencies needs to be installed manuelly. See dependency secion below.
+
+## Testing the installation
 When the dependencies are all installed CanSNPer can be run as it is from the 
 shell.
 
@@ -31,20 +52,21 @@ directory.
 More on how to run CanSNPer in its various modes can be found in the README 
 file that came with the distribution.
 
-CanSNPer has only been tested on Linux, but feel free to tinker with setting up 
+CanSNPer has been tested on Linux and MacOS (OSX), but feel free to tinker with setting up 
 a working version on your favorite OS. Mauve is available on other platforms.
 
 ##Dependencies
 Software that must be installed before running CanSNPer:
 
 [Python (2.7.X)](http://www.python.org/getit/)  
-Most Linux distributions come with Python installed.
+Most Linux distributions come with Python installed. However we recommend using 
+[Conda](http://conda.pydata.org/docs/) to setup a flexible Python environment. 
 
 [ETE2](http://ete.cgenomics.org/)  
 ETE2 has a number of additional dependencies, listed in their install 
 notes. Most notably, there are several dependencies that are not needed 
 for CanSNPer, but they may raise warnings as ETE2 is loaded. Note that
-Qt > 5 is needed to run ETE2.
+Qt < 5 is needed to run ETE2.
 
 [NumPy](http://www.numpy.org/)  
 Simple install instructions are available for this package.

README.md

@@ -1,8 +1,11 @@
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/cansnper/README.html)
+
 ##Installing CanSNPer 
 CanSNPer is written in Python and requires Python installed as well as several 
-dependencies listed in the INSTALL document. Consult that file for detailed 
-installation instructions. When the dependencies are all installed CanSNPer can 
-be run as it is from the shell.
+dependencies. The easiest way to install CanSNPer is using 
+[Bioconda conda](https://bioconda.github.io/recipes/cansnper/README.html) channel 
+or with pip. Consult the INSTALL document for detailed installation instructions. 
+When the dependencies are all installed CanSNPer can be run as it is from the shell.
 
 ##Running CanSNPer
 All CanSNPer runs start with the main CanSNPer script. Following installation,