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pdimens authored Jun 24, 2023
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[![Anaconda-Server Badge](https://anaconda.org/bioconda/harpy/badges/platforms.svg)](https://anaconda.org/bioconda/harpy)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/harpy/badges/downloads.svg)](https://anaconda.org/bioconda/harpy)

Haplotagging Data Processing Pipeline, getting you from raw reads to genotypes or phased haplotypes or your money back.
Haplotagging Data Processing Pipeline, getting you from raw reads to genotypes/phased haplotypes or your money back.

## 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).

### 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 `conda install` code:
```bash
conda install -c bioconda harpy

# or ⚡ mamba ⚡#
mamba install -c bioconda -c conda-forge harpy
```

### into new conda environment
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` (`-n harpy`) and installs harpy into it. You can name this environment whatever you like.
**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` and installs harpy into it. You can name this environment whatever you like by changing `-n harpy` to `-n somethingelse`.
```bash
conda create -n harpy -c bioconda harpy

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```

### Activate the harpy environment
Once installed with one of the methods above, activate the conda environment you installed harpy into with
Once conda/mamba finishes, activate the conda environment you installed harpy into with
```bash
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.


### 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 `conda install` code:
```bash
conda install -c bioconda harpy

# or ⚡ mamba ⚡#
mamba install -c bioconda -c conda-forge harpy
```

#### EMA note
The version of [EMA](https://github.com/arshajii/ema) bundled in this repository (`ema-h`) is a [fork](https://github.com/EdHarry/ema/tree/haplotag) of the orignal EMA modified to work with Generation 1 haplotag beadtags (AxxCxxBxxDxx). Work is underway to merge haplotag support and publish a new version of EMA to remove reliance on this precompiled fork.

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