Introduction

Pipelines
This repository contains the following pipelines:
Imputation
RNA-seq (Experimental)
It also contains pipelines with their own repo's like:
​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​
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

Environment setup with easybuild

Last modified 4yr ago