Haplotag Data Processing Pipeline. Getting you from raw reads to genotypes/phased haplotypes or your money back.

📥 Install

To avoid dependency conflicts with an existing environment, it is 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.

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

⚪️ install into an existing conda environment ⚪️

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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:

mamba install -c bioconda -c conda-forge harpy

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

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

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🌟 Activate the harpy environment

Once conda/mamba finishes, activate the conda/mamba environment you installed harpy into 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.

⚡ Usage

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

harpy