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INSTALL.md

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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 >= 3.6
  • 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/master.zip

$ unzip master.zip

$ cd F-Seq2-master

# install all dependencies listed below

$ python setup.py install

Integration test

$ cd Fseq2

$ python setup.py test

This may take 1 min

Packages installed after installation

  • numpy >= 1.15.4
  • scipy >= 1.1.0
  • pandas >= 0.24
  • statsmodels
  • KDEpy
  • pybedtools
  • pyBigWig
  • h5py
  • matplotlib