Installing Nextflow locally

Nextflow is a powerful workflow management system that simplifies the process of writing and executing complex data analysis pipelines. This guide will help you install Nextflow on any of the RCAC clusters, enabling you to run bioinformatics workflows efficiently.

Installation steps

1. Check java version

   module --force purge
   module load openjdk
   java -version

   Ensure you have Java 17 or later installed. If not, follow guide to install Java.

2. Install Nextflow

   cd ~
   curl -s https://get.nextflow.io | bash

   This command installs Nextflow in your current directory.

3. Make Nextflow executable and add it to your PATH

   chmod +x nextflow
   mv nextflow ~/bin/
   echo 'export PATH=$PATH:~/bin' >> ~/.bashrc
   source ~/.bashrc

   This makes nextflow accessible from anywhere in your terminal.

4. Verify Nextflow installation

   nextflow -version

Tip

To update Nextflow in the future, you can run nextflow self-update in your terminal.

FAQs

1. What to do when java is not available? [click to expand]

If java version you need is not available, you can install it using the following steps:

1. Install SDKMAN

   cd $HOME
   curl -s https://get.sdkman.io | bash

2. Load SDKMAN

   source "$HOME/.sdkman/bin/sdkman-init.sh"

3. Install Java 17

   sdk install java 17.0.8-tem

4. Verify Java installation

   java -version