Installation

IsoQuant requires a 64-bit Linux system or Mac OS and Python (3.8 and higher) to be pre-installed on it. You will also need

Installing from conda

IsoQuant can be installed with conda:

conda create -c conda-forge -c bioconda -n isoquant python=3.8 isoquant

To obtain IsoQuant you can download repository and install requirements.
Clone IsoQuant repository and switch to the latest release:

git clone https://github.com/ablab/IsoQuant.git
cd IsoQuant
git checkout latest

Install requirements:

pip install -r requirements.txt

You also need samtools and minimap2 to be in the $PATH variable.

To verify IsoQuant installation type

isoquant.py --test

to run on toy dataset.
If the installation is successful, you will find the following information at the end of the log:

=== IsoQuant pipeline finished ===
=== TEST PASSED CORRECTLY ===