__
    .,-;-;-,. /'_\
  _/_/_/_|_\_\) /
'-<_><_><_><_>=/\
  `/_/====/_/-'\_\
   ""     ""    ""

Source code is available on GitHub.

Requirements

• Linux or macOS. On Windows, consider using Ubuntu for WSL. BusyBox is not supported.
• POSIX-compliant login shell: bash, zsh, dash, or ksh93; csh, fish, nushell, powershell, and tcsh are not supported.
• Bash 4+ and Python 3.8+. These will be bootstrap installed into ~/.local/share/koopa-bootstrap automatically when necessary.
• Core utilities: cp, curl, find, git, grep, mkdir, mktemp, mv, rm, sed, tar, unzip.

macOS

Xcode Command Line Tools are required.

xcode-select --install

The command line tools will install into /Library/Developer/CommandLineTools.

Debian / Ubuntu

if [ "$(id -u)" -eq 0 ]
then
    apt-get update
    apt-get --quiet --yes install sudo
fi
sudo apt-get update
sudo apt-get \
    --no-install-recommends \
    --quiet \
    --yes \
    install \
        bash \
        build-essential \
        ca-certificates \
        coreutils \
        curl \
        findutils \
        git \
        locales \
        lsb-release \
        procps \
        python3 \
        unzip

Fedora / RHEL

if [ "$(id -u)" -eq 0 ]
then
    dnf -y install sudo
fi
sudo dnf -y install \
    automake \
    bash \
    coreutils \
    curl \
    findutils \
    gcc \
    git \
    make \
    procps \
    python3 \
    unzip

Installation

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 dotfile configuration and whether your shell profile configuration file should be modified.

sh -c "$(curl -LSs https://koopa.acidgenomics.com/install)"

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

install="$(mktemp)"
curl -LSs -o "$install" https://koopa.acidgenomics.com/install
chmod +x "$install"
"$install"

Here’s how to install koopa non-interactively, which is intended primarily for building Docker images.

curl -LSs https://koopa.acidgenomics.com/install \
    | sh -s -- --non-interactive

Enable activation

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

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

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

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.

• bash: .bashrc, .bash_profile
• dash: .profile
• ksh93: .profile
• zsh: .zshrc

Verify installation

Restart the shell. Koopa should now activate automatically at login. You can verify this with command -v koopa.

Install applications

Koopa supports installation of many bioinformatics applications. Currently supported apps can be see using TAB autocompletion with koopa install <TAB>. To install the recommended default stack, run koopa install-default-apps, or install all supported apps with koopa install-all-apps.

The current system configuration can be checked with koopa system check. This is powered internally by our r-koopa package, which requires R to be installed.

Update dotfiles

Configure the current user’s environment using our dotfiles repo, which is currently powered by chezmoi.

koopa install dotfiles
koopa configure user dotfiles

Troubleshooting

If you are installing behind a corporate firewall, you may need to export http_proxy in the current shell session for koopa and bootstrap dependencies to download successfully. Please file an issue on GitHub if you encounter any connection issues during installation.

© 2018-pres. Acid Genomics LLC.