Installing probNORM¶

probNORM can be installed through conda, pypi and from the repository.

Required


Python:	version 3.6 or greater (Python 3 is supported). If you’re setting up Python for the first time, the Anaconda Python distribution is highly recommended.
Libraries:	pysam, numpy, scipy
BEDTools:	The version is not important, but later versions will have more features so it’s a good idea to get the latest. Follow the instructions at https://github.com/arq5x/bedtools2 to install, and make sure the programs are on your path. That is, you should be able to call bedtools from any directory.

Conda installation¶

This is by far the easiest option. If you’re using the Anaconda Python distribution, then the following will install probNORM:

conda install -c bioconda probNORM

You can also install probNORM together with BEDTools via conda:

conda install -c bioconda probNORM bedtools

Both commands will install probNORM from the bioconda/conda channel and automatically makes sure that dependencies are installed.

Otherwise, read on for installation on other platforms and in other environments.

probNORM is on PyPI under the probnorm name, so you can install via pip like most Python packages.

Depending on your Python installation, this may require admin rights:

pip install probnorm

Get probNORM from repository

Download by clonning this repository:

git clone https://github.com/zywicki-lab/probNORM.git

or download a .zip package and unpack it:

wget https://github.com/zywicki-lab/probNORM/archive/refs/heads/main.zip

unzip main.zip

Install python dependencies:
You can install them automatically with the following command:
```
pip3 install requirements.txt
```
or one-by-one using standard pip installation command, i.e.
```
pip3 install pysam numpy scipy
```
Install BEDtools:
Following command installs mentioned software system-wide.
```
sudo apt-get install bedtools
```