01 - Hydra cluster setup

Access to the Hydra cluster

You will need an account to access the Smithsonian Hyrda computing cluster. Instructions are available here.

First time setup

We have submitted a request to the Hydra team for installation of a Nextflow module. But for now, you will need to install your own copy of Nextflow on the cluster. Login to Hydra and run the following.

# Nextflow installation instructions
# from https://www.nextflow.io/docs/latest/install.html
cd ~
# load Java module, needed by Nextflow
module load tools/java/21.0.2
# install Nextflow
curl -s https://get.nextflow.io | bash 
# make Nextflow executable
chmod +x nextflow 

There will now be an executable nextflow file in your home directory. You should move it to a location that is in your PATH. For example:

 # create bin directory, if needed
mkdir ~/bin
# move nextflow to bin directory
mv ~/nextflow ~/bin/nextflow 
# add bin directory to PATH, in case it's not already there
echo 'export PATH="${HOME}/bin:${PATH}"' >> ~/.bashrc 
# reload your bash configuration file
source ~/.bashrc

This should allow you to call nextflow from anywhere on the cluster.

Important

You must load the Hydra Java module (module load tools/java/21.0.2) whenever you wish to use Nextflow.