installation.rst

Installation

ProkFunFind dependencies

ProkFunFind has several dependencies:

• The Blast suite of program (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
• The program Hmmer version 3.1 (http://hmmer.janelia.org/).

All these programs should be installed (e.g., in the $PATH) in order to use ProkFunFind.

Additional python packages will be installed during the ProkFunFind installation including:

• biopython
• scikit-learn
• configparser
• typing
• importlib
• argparse
• numpy
• six

Archive overview

• Folder structure in ProkFunFind package:
• bin => contain the executable (prokfunfind.py)
• data => the preconfigured data for each function
• doc => the documentation in html and pdf
• test => all needed for unit tests
• ProkFunFind => the ProkFunFind python library
• setup.py => the installation script

Installation Instructions

Download ProkFunFind

git clone https://github.com/nlm-irp-jianglab/ProkFunFind.git

Install ProkFunFind

We recommend installing ProkFunFind within a python virtual environment.

conda create -n ProkFun python=3
conda activate ProkFun
pip install ./ProkFunFind