Haplotagging Data Processing Pipeline. Getting you from raw reads to assemblies, genotypes, or phased haplotypes or your 💰 back.
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.
conda create -n harpy -c bioconda -c conda-forge harpy⚪️ install into an 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::harpyOr provide -n envname to install it into an existing environment named envname
conda install -n envname -c conda-forge bioconda::harpyconda update -c conda-forge bioconda::harpyOnce conda/mamba finishes, activate the conda/mamba environment you installed harpy into with
conda activate env_namewhere env_name is the name of that environment. After doing so, the harpy executable should be callable from your path.
Just call harpy or harpy --help on the command line to get started!
harpyNo 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.