Installation

Conda

To install with conda, just run:

conda config --add channels bioconda
conda config --add channels conda-forge
conda install pling

From source

Start with:

git clone https://github.com/iqbal-lab-org/pling.git && cd pling

From here you can install dependancies using conda with the env.yaml file, or whichever method you prefer. To install dependancies with conda, do:

conda env create -f env.yaml
conda activate pling

and then finally install pling with:

python -m pip install .

Installing optional dependancies

By default, the DCJ-Indel distances are calculated with the open source solver GLPK. Optionally, pling can use Gurobi for its calculations, but this dependancy is not included in the usual pling installation. This is because Gurobi is a commercial software which requires a license, which is free for academic purposes. Information on obtaining this license can be found here: https://www.gurobi.com/academia/academic-program-and-licenses/. Gurobi can then be installed via conda as follows:

conda config --add channels https://conda.anaconda.org/gurobi
conda install gurobi=10.0.1