# Install

# Install Harpy

conda or mamba
- we strongly recommend you use conda 23.10 (or later) or mamba
- if using mamba, replace conda with mamba in the instructions below

Harpy is hosted on Bioconda! That means to install it, you just need to have conda (or mamba) on your Linux-based system and install it with a simple command. You can install Harpy into an existing environment or create a new one for it (recommended).

# install into a new environment

# ✨recommended✨

The code snippet below creates a new environment called harpy (the -n harpy part) and installs harpy into it from the bioconda channel (-c bioconda part). You can name this environment anything (e.g. haplotagging, jeanclaudevandamme, etc.).

install harpy
conda create -n harpy -c bioconda -c conda-forge harpy

Once conda finishes the install, you can activate the environment (with whatever -n <env_name> you gave it) and harpy will be callable from the command line.

activate harpy environment
conda activate <env_name>

# install into an existing evironment

If you want to install harpy into an existing environment, then with an environment already activated (via conda activate <env_name>) simply use the conda install command and harpy will be callable from the command line.

install harpy
conda install -c bioconda -c conda-forge harpy

# Update Harpy

conda or mamba
Harpy installed into an existing conda enviroment

If you want to update Harpy, the process is quite similar:

update harpy
conda activate <env_name>
conda update -c conda-forge bioconda::harpy