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).
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
# 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
# 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