# Install Harpy

conda or mamba
- if using conda, we strongly recommend using version 23.10 or later
- if using mamba, replace conda with mamba in the instructions below
pixi
- relatively new kid on the block-- think of it as the next-gen of conda
- it's a little different, but it's lightning fast and very sensible to use

Harpy is hosted on Bioconda, which means you just need to have either conda or pixi on your Linux-based system to install it. This page details both the conda and pixi installation approaches.

# 🐍 Conda

It's best to create a new environment for a harpy installation. The code below creates a new conda/mamba environment called harpy (via -n harpy) and installs harpy into it. You can name this environment whatever you like using the -n somename argument.

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

Once conda/mamba finishes, activate the harpy conda/mamba environment with:

conda activate env_name

where env_name is the name of that environment. After doing so, the harpy executable should be callable from your path.

Alternatively, you can create the environment locally within a specific project folder, just swap -n harpy for -p path/to/workdir/harpy, which creates the environment in that specific folder (e.g. potato_blight/harpy).

conda create -p path/to/workdir/harpy -c bioconda -c conda-forge harpy

If you wish to install harpy and its dependencies into an existing environment, activate that environment and execute this installation code:

conda activate env_name
conda install -c conda-forge bioconda::harpy

Or provide -n env_name to install it into an existing environment named env_name

conda install -n env_name -c conda-forge bioconda::harpy

Activate the environment and run conda update:

conda update -c conda-forge bioconda::harpy

# ⚡ Conda Usage

Activate the conda environment with Harpy and call harpy or harpy --help on the command line to get started

activate the environment
conda activate harpy_env

call harpy
harpy

Activate the conda environment with Harpy and call harpy or harpy --help on the command line to get started

activate the environment
conda activate path/to/harpy_env

call harpy
harpy

# 🌟 Pixi

If you prefer Pixi (it's pretty good, you should try it), you can install Harpy to be accessible in your PATH, i.e. a "global" installation:

pixi global install -c conda-forge -c bioconda harpy

add pixi to PATH

Make sure ~/.pixi/bin is in your PATH:

~/.zshrc or ~/.bashrc (or equivalent)
export PATH=~/.pixi/bin:$PATH

Likewise, you can do an installation into a local project directory:

pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add harpy

If installed via Pixi, you can update Harpy with pixi update:

pixi global update harpy

# project dir has the pixi.toml file
cd path/to/projectdir
pixi update harpy

# ⚡ Pixi Usage

If installed globally, just call harpy or harpy --help on the command line:

harpy

Navigate to project directory
cd path/to/workdir

Then:

call harpy from within pixi environment
pixi shell

harpy --help

call harpy with pixi prefix
pixi run harpy