Installation of uap

Prerequisites

The installation requires Python’s virtualenv. It is a tool to create isolated Python environments. So, please install it if its not already installed.:

$ sudo apt-get install python-virtualenv
OR
$ sudo pip install virtualenv

In addition to this git and graphviz are also needed.

The uap installation does not include all necessary tools for the data analysis. It is expected that the required tools are already installed.

Downloading the Software

Download the software from uap's github repository. like this:

$ git clone https://github.com/kmpf/uap.git

Setting Up Python Environment

After cloning the repository, change into the created directory and run the bootstrapping script bootstrap.sh:

$ cd uap
$ ./bootstrap.sh

The script creates the required Python environment (which will be located in ./python_env/). Afterwards it installs PyYAML, NumPy, biopython and psutil into the freshly created environment. There is no harm in accidentally running this script multiple times.

Making uap Globally Available

uap can be used globally. On Unix-type operating systems it is advised to add the installation path to your $PATH variable. Therefore change into the uap directory and execute:

$ pwd

Copy the output and add a line to your ~/.bashrc or ~/.bash_profile like the following and replace <uap-path> with the copied output:

PATH=$PATH:<uap-path>

Finally, make the changes known to your environment by sourcing the changed file:

$ source ~/.bashrc
$ source ~/.bash_profile