MOLGENIS Pipelines
  • Introduction
  • Release Notes
  • Environment setup with easybuild
    • Install environment
  • NGS_DNA
  • NGS_RNA
    • Install pipeline
    • Dependencies
    • Run
    • Workflow
    • Protocols
  • MOLGENIS Compute
    • Quickstart
    • Parameters
    • Reference
    • Read more
  • MOLGENIS CoNVaDING
    • CoNVaDING
Powered by GitBook
On this page
  • Pipelines
  • How to get started
  • Step 1: download Molgenis Compute
  • create dir
  • download
  • test
  • Step 2: clone this repo
  • For read/write access:

Introduction

NextEnvironment setup with easybuild

Last updated 6 years ago

Pipelines

This repository contains the following pipelines:

  • Imputation

  • RNA-seq (Experimental)

It also contains pipelines with their own repo's like:

  • 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

Step 1: download Molgenis Compute

  • Download the latest MOLGENIS Compute from

  • 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
NGS_DNA
go here
https://github.com/molgenis/molgenis-compute/releases