Haplotagging Data Processing Pipeline. Getting you from raw reads to assemblies, genotypes, or phased haplotypes or your 💰 back.

📥 Install

🐍 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.

⬇️ install as local conda environment

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).

# for local project directory
conda create -p path/to/workdir/harpy -c bioconda -c conda-forge harpy

⬇️ install into existing conda environment

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

conda install -c conda-forge bioconda::harpy

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

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

⬆️ updating harpy

If installed via conda, you can update Harpy by activating the environment and running conda update like so:

conda update -c conda-forge bioconda::harpy

🌟 Pixi

If you prefer Pixi (it's pretty good, you should try it), you can install Harpy to be accessible in your PATH-- just make sure ~/.pixi/bin is in your PATH:

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

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

⬇️ install as local environment

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

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

After that finishes, you can activate the environment with:

pixi shell

Or run harpy by prefixing it with pixi run:

pixi run harpy

⬆️ updating harpy

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

# global install
pixi global update harpy

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

⚡ Usage

Just call harpy or harpy --help on the command line to get started!

harpy

🌈 Getting Started

No data? No problem! Harpy lets you simulate genomic variants from an existing genome and can also create haplotag data from an existing genome! You can see what haplotag data (and Harpy) are like without paying a cent! A simple tutorial on simulating both of these can be found here.