Installation

Requirements

  • Python 3.6

  • HiCExplorer 3.5

  • cooler 0.8.9

  • HiCMatrix 14

  • sparse-neighbors-search 0.6

Command line installation using conda

The fastest way to obtain Python 3.6 together with numpy and scipy is via the Anaconda Scientific Python Distribution. Just download the version that’s suitable for your operating system and follow the directions for its installation. All of the requirements for scHiCExplorer can be installed in Anaconda with:

$ conda install schicexplorer python=3.6 -c bioconda -c conda-forge

We strongly recommended to use conda to install scHiCExplorer.

Command line installation with source code

1. Download source code

$ git clone https://github.com/joachimwolff/scHiCExplorer.git

2. Install dependencies:

$ cd scHiCExplorer
$ conda install --file requirements.txt -c bioconda -c conda-forge

3. Install the source code:

$ python setup.py install