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