Installation

Fivepseq is designed to run on Unix systems with python 2.7 or python 3.x.

Dependencies

To set up fivepseq, the following python packages need to be pre-installed manually using pip (if you don’t have pip you may install it as described here ).

Paste the following lines into the shell terminal:

pip install --upgrade numpy pysam cython
pip install plastid

In order to enable exporting vector and portable image files, you’ll also need to have phantomjs installed as follows:

conda install phantomjs selenium pillow

Fivepseq installation

Clone the project from github:

git clone https://github.com/lilit-nersisyan/fivepseq.git

Navigate into the fivepseq directory and install:

python setup.py install

To check if fivepseq was installed correctly, type the following in the command line:

fivepseq --version

This should display the currently installed version of fivepseq. To display commandline arguments you may type:

fivepseq --help

Fivepseq module installation

In order to install fivepseq as a python module, you may use pip:

pip install fivepseq