.,-;-;-,. /'_\
  _/_/_/_|_\_\) /
   ""     ""    ""


Shell bootloader for bioinformatics.


Source code is available on GitHub.


Dependencies for executable scripts:


Ensure that curl, git, and sudo are installed before proceeding.


The install script will prompt to determine whether you want a shared install for all users, or for the current local user only. It will also ask about dot file configuration and whether your shell profile configuration file should be modified.

bash -c "$(curl -sSL https://koopa.acidgenomics.com/install)"

Alternatively, download the install script as a temporary file and then execute.

curl -sSL -o "$install" https://koopa.acidgenomics.com/install
chmod +x "$install"


This is intended primarily for building Docker images.

curl -sSL https://koopa.acidgenomics.com/install \
    | bash -s -- --non-interactive

Update shell configuration

Note that this step is not required for a shared installation on Linux, which writes a configuration file into /etc/profile.d instead.

To activate koopa on login, add these lines to your shell configuration file:

# koopa shell
# https://koopa.acidgenomics.com/
# shellcheck source=/dev/null
if [ -f "${XDG_CONFIG_HOME}/koopa/activate" ]
    . "${XDG_CONFIG_HOME}/koopa/activate"

Not sure where to source activate in your configuration? Here are some general recommendations, in order of priority for each shell. These can differ depending on the operating system, so refer to your shell documentation for details.

Check installation

Restart the shell. Koopa should now activate automatically at login. You can verify this with command -v koopa. Next, check your environment dependencies with koopa check. To obtain information about the working environment, run koopa info.

Docker images

These images contain koopa along with other useful bioinformatics software.

Pre-installed software


These images only contain koopa installed on top of the base Docker image.