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INSTALL.md

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##Installing CanSNPer CanSNPer is written in Python and requires Python installed as well as several 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.

Bioconda

With an activated Bioconda channel (see 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.

git clone https://github.com/adrlar/CanSNPer.git
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.

To begin with, try:

CanSNPer --help

If there are no errors and you see the help text printed, CanSNPer is working correctly and you can go on to do your analysis.

If all dependencies are installed you can also run CanSNPer without running the setup.py. This is done by running python CanSNPer -h from within the CanSNPer 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 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)
Most Linux distributions come with Python installed. However we recommend using Conda to setup a flexible Python environment.

ETE2
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.

NumPy
Simple install instructions are available for this package.

progressiveMauve
The progressiveMauve binary must be in the PATH or specifically set in the CanSNPer.conf file.