Pipelines for NGS, imputation, gwas, ...
Shell FreeMarker TeX Other
Latest commit a79238e Oct 11, 2016 @freerkvandijk freerkvandijk committed on GitHub Merge pull request #586 from npklein/master
GCCXX error fix, use gzipped vcf (phasing pipeline)


MOLGENIS 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 visit https://github.com/molgenis/molgenis_apps-legacy/blob/testing/doc/compute/01_compute_introduction.md

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