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Update README.md
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vcfdist has been added to bioconda
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TimD1 authored Feb 18, 2024
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Expand Up @@ -68,7 +68,21 @@ Please cite the following works if you use vcfdist:

## Installation

### Option 1: GitHub Source
### Option 1: bioconda
If you have `conda` installed with the `bioconda` channel (instructions [here](https://bioconda.github.io/)), run:
```bash
conda install vcfdist
```

### Option 2: Docker image
A pre-built Docker Hub image can be downloaded from <a href="https://hub.docker.com/r/timd1/vcfdist">here</a> using:
```bash
sudo docker pull timd1/vcfdist
sudo docker run -it timd1/vcfdist:latest vcfdist --help
```


### Option 3: GitHub source
vcfdist is developed for Linux and its only dependencies are GCC v9.1+ and HTSlib v1.17. If you don't have HTSlib already, please set it up as follows:
```bash
> wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
Expand All @@ -90,13 +104,6 @@ If you do already have HTSlib installed elsewhere, make sure you've added it to
vcfdist v2.4.0
```

### Option 2: Docker Image
A pre-built Docker Hub image can be downloaded from <a href="https://hub.docker.com/r/timd1/vcfdist">here</a> using:
```bash
sudo docker pull timd1/vcfdist
sudo docker run -it timd1/vcfdist:latest vcfdist --help
```

## Usage

The <a href="./demo">`demo`</a> directory contains a <a href="./demo/demo.sh">demo script</a> (shown below) and all required inputs. It operates on the first 5 million bases on `chr1`, and should run in about 3 seconds.
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