This repository contains the following pipelines:
It also contains pipelines with their own repo's like:
In addition it contains protocols that may be re-used between different (versions of a) pipeline(s).
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
Download the latest MOLGENIS Compute from https://github.com/molgenis/molgenis-compute/releases
Currently (April 2017) MOLGENIS Compute v1.4 (16.11.1)
mkdir mycompute cd mycompute
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
git clone https://github.com/molgenis/molgenis-pipelines.git