installation.md

nfcore/rnaseq Installation

To start using the nfcore/rnaseq pipeline, there are three steps described below:

1. Install Nextflow
2. Install the pipeline
3. Configure the pipeline
   • Local configuration
   • Amazon Web Services (aws)
   • Swedish UPPMAX clusters
   • Swedish cs3e Hebbe cluster
   • Tübingen QBiC
   • Adding your own system

1) Install NextFlow

Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:

# Make sure that Java v7+ is installed:
java -version

# Install Nextflow
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

You need NextFlow version >= 0.24 to run this pipeline.

See nextflow.io and NGI-NextflowDocs for further instructions on how to install and configure Nextflow.

2) Install the Pipeline

This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if nf-core/rnaseq is specified as the pipeline name.

Offline use

If you need to run the pipeline on a system with no internet connection, you will need to download the files yourself from GitHub and run them directly:

wget https://github.com/nf-core/rnaseq/archive/master.zip
unzip master.zip -d /my-pipelines/
cd /my_data/
nextflow run /my-pipelines/rnaseq-master