01 - bash setup script

#!/bin/bash
# SI NMNH MitoPilot workshop
# December 11, 2025
# https://dmacguigan.github.io/MitoPilot_workshop_2025/
# author: Dan MacGuigan
# macguigand@si.edu

# MitoPilot setup script to install dependencies

# 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 
 # 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