install all dependencies listed below

Installation

Binary installers for the latest released version are available at the python package index and on conda.
The source code is currently hosted on GitHub at: https://github.com/Boyle-Lab/F-Seq2

Prerequisites

• python >= 3.9
• bedtools >= 2.29.0 (required by pybedtools)

Prepare a conda environment (optional)

$ conda create --name fseq2_env python=3.6
$ conda activate fseq2_env

Install from binary installer

# PyPI
$ pip install fseq2

# or conda
$ conda install -c bioconda -c dmentipl -c samzhao fseq2

Install from source

$ wget https://github.com/Boyle-Lab/F-Seq2/archive/refs/tags/v2.0.4.zip

$ unzip master.zip

$ cd F-Seq2-master

# install all dependencies listed below
$ pip install numpy==1.26.4
$ pip install .

Integration test

$ cd Fseq2

$ pytest

This may take 1 min

Packages installed after installation

• numpy == 1.26.4
• scipy >= 1.1.0
• pandas >= 0.24
• statsmodels
• KDEpy
• pybedtools
• pyBigWig
• h5py
• matplotlib
• cython