2. Installing Pseudofinder - filip-husnik/pseudofinder GitHub Wiki

This page will guide you through setting up Pseudofinder and its dependencies on your machine.

Easy Installation

Easy installation requires python3 and Conda already installed. This will install pseudofinder into your $PATH and take care of all dependencies.

git clone https://github.com/filip-husnik/pseudofinder.git
cd pseudofinder
bash setup.sh
conda activate pseudofinder

# when finished with using pseudofinder
conda deactivate

Manual Installation

If you prefer to not use Conda, these are the dependencies that you must have to properly run Pseudofinder.

Installation of python3, pip3, git (optional), and ncbi-blast+ on Ubuntu (as an administrator):

sudo apt-get update

sudo apt-get install python3
sudo apt-get install python3-pip
sudo apt-get install ncbi-blast+
sudo apt-get install git

Installation of 3rd party python3 libraries on Ubuntu (as an administrator):

sudo pip3 install biopython
sudo pip3 install plotly
sudo pip3 install pandas
sudo pip3 install numpy
sudo pip3 install reportlab
etc...

Clone the up to date pseudofinder.py code from github (no root access required):

git clone https://github.com/filip-husnik/pseudo-finder.git

Or download a stable release:

https://github.com/filip-husnik/pseudofinder/releases/tag/v1.1.0