MOLGENIS pipelines

Pipelines

This repository contains the following pipelines:

• Alignment
• Imputation
• GWAS
• RNA-seq (Experimental)

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 http://www.molgenis.org/wiki/ComputeStart
# Currently (March 2013) http://www.molgenis.org/raw-attachment/wiki/ComputeStart/molgenis_compute-fb05467.zip

# create dir
mkdir mycompute
cd mycompute

# download
wget http://www.molgenis.org/raw-attachment/wiki/ComputeStart/molgenis_compute-fb05467.zip
unzip molgenis_compute-\<version>.zip
mv molgenis_compute-\<version>/* .  

# test  
sh molgenis_compute.sh  

Step 2: clone this repo

# For read/write access:
git clone https://github.com/molgenis/molgenis-pipelines.git
# Alternatively to only download the pipelines use:
wget https://github.com/molgenis/molgenis-pipelines/archive/master.zip
unzip master