Shell bootloader for bioinformatics.
Bash shell running on either Linux or macOS is currently supported.
First, clone the repository:
git clone https://github.com/steinbaugh/koopa.git ~/koopa
Second, add these lines to
# koopa shell # https://github.com/steinbaugh/koopa source ~/koopa/bin/koopa activate
Koopa should now activate at login. To obtain information on the current working enviroment, simply run
High-performance computing (HPC) environment
Since workload managers can spawn non-interactive login shells for new jobs, we recommend additionally symlinking
~/.bash_profile. For non-interactive login shells, koopa doesn't attempt to print any messages, so the shell remains clean.
To launch an interactive job on an HPC cluster, simply run the
interactive script. All arguments are optional, but generally we recommend setting the number of cores, memory, and time.
interactive --cores=[N] --mem=[GB] --time=[D-HH::MM]
For example, here's how to start an interactive job on an HPC running Slurm, which will run for 6 hours using 2 cores and 16 GB of RAM total (i.e. 8 GB per core).
interactive --cores=2 --mem=16 --time=0-06:00
For more information on supported arguments, consult