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koopa 🐢

Build Status Project Status: Active – The project has reached a stable, usable state and is being actively developed.

High-performance computing shell bootloader for bioinformatics.

Installation

Connect to your high-performance computing (HPC) cluster and clone our git repository.

git clone https://github.com/steinbaugh/koopa.git ~/koopa

Add these lines to your .bashrc file:

# koopa shell
# https://github.com/steinbaugh/koopa
if [[ -n "$PS1" ]] && [[ -f ~/koopa/koopa.sh ]]; then
    . ~/koopa/koopa.sh
fi

To also load koopa on a login node, we recommend symlinking your .bashrc file to .bash_profile:

ln -s ~/.bashrc ~/.bash_profile

Interactive session

To launch an interactive session, simply run:

koopa interactive -c <cores> -m <memory> -t <time>

For example, here's how to start an interactive session for 6 hours using 2 cores and 8 GB of RAM per core, on an HPC using the slurm scheduler:

koopa interactive -c 2 -m 8 -t 0-06:00