> For the complete documentation index, see [llms.txt](https://molgenis.gitbook.io/molgenis-pipelines/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://molgenis.gitbook.io/molgenis-pipelines/master.md).

# Introduction

## Pipelines

This repository contains the following pipelines:

* Imputation
* RNA-seq (Experimental)

It also contains pipelines with their own repo's like:

* [NGS\_DNA](https://www.gitbook.com/book/molgenis/ngs_dna)
* NGS\_RNA

In addition it contains protocols that may be re-used between different (versions of a) pipeline(s).

## How to get started

Below we explain (step 1) how to download and deploy Molgenis Compute. This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data. Next, we explain (step 2) how you can download even more pipelines and protocols by cloning this repo.

For a 'walkthrough' tutorial on Molgenis Compute, please [go here](https://molgenis.gitbooks.io/molgenis-pipelines/content/pipelines/mc-start.html)

## Step 1: download Molgenis Compute

* Download the latest MOLGENIS Compute from <https://github.com/molgenis/molgenis-compute/releases>
* Currently (April 2017) MOLGENIS Compute v1.4 (16.11.1)

### create dir

```
mkdir mycompute
cd mycompute
```

### download

```
wget https://github.com/molgenis/molgenis-compute/releases/download/v16.11.1/molgenis-compute-v16.11.1.tar.gz
tar -xzvf molgenis-compute-v16.11.1.tar.gz
```

### test

```
sh molgenis_compute.sh
```

## Step 2: clone this repo

### For read/write access:

```
git clone https://github.com/molgenis/molgenis-pipelines.git
```