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pdimens authored Aug 24, 2023
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## Install
Now hosted on [Bioconda](https://anaconda.org/bioconda/harpy)! Install harpy on Linux-based systems using [conda](https://mamba.readthedocs.io/en/latest/installation.html) or [mamba](https://mamba.readthedocs.io/en/latest/micromamba-installation.html#umamba-install) (**recommended**).
Now hosted on [Bioconda](https://anaconda.org/bioconda/harpy)! Install harpy on Linux-based systems using [conda](https://mamba.readthedocs.io/en/latest/installation.html) or [mamba](https://mamba.readthedocs.io/en/latest/micromamba-installation.html#umamba-install) (**strongly recommended**).

### Install into new environment (recommended)
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 environment called `harpy` (via `-n harpy`) and installs harpy into it. You can name this environment whatever you like using the `-n somename` argument.
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│ trim Remove adapters and quality trim sequences │
│ variants Call variants (SNP/SV) from samples │
╰───────────────────────────────────────────────────────────────╯
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