Installation

deepDegron has only been tested on linux operating systems. We recommend that you use python 3.7 to run deepDegron.

Installation by PIP

The easiest way to install deepDegron is to use PIP.

$ pip install deepDegron
$ pyensembl install --release 75 --species human  # download human hg19 reference data
$ pyensembl install --release 95 --species human  # download human hg38 reference data

Installing from source

Releases

First download the deepDegron source code on on github.

Once downloaded, please change to the top-level directory in the deepDegron source code.

Installing dependencies

We recommend using conda to install the deepDegron dependencies.

$ conda env create -f environment.yml  # create environment for deepDegron
$ source activate deepDegron # activate environment for deepDegron
$ pyensembl install --release 75 --species human  # download human reference data
$ python setup.py install  # install deepDegron

Make sure the deepDegron environment is activated when you want to run deepDegron.

An alternative way to install the python dependencies is to use pip.

$ python -m pip install --upgrade pip
$ pip install -r requirements.txt  # install required packages
$ pyensembl install --release 75 --species human  # download human reference data
$ python setup.py install  # install deepDegron