Shell bootloader for bioinformatics.
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README.md

koopa 🐢

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

Shell bootloader for bioinformatics.

Installation

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 ~/.bash_profile:

# 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 koopa info.

High-performance computing (HPC) environment

Koopa currently supports Slurm and IBM Platform LSF workload managers.

Since workload managers can spawn non-interactive login shells for new jobs, we recommend additionally symlinking ~/.bashrc to ~/.bash_profile. For non-interactive login shells, koopa doesn't attempt to print any messages, so the shell remains clean.

Interactive jobs

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 interactive --help.