domagi is a DuckDB-powered clone of odgi, the pangenome manipulation tool.

Installation

Using Guix

You can download the latest development version of domagi using Guix. Put the following into a file channels.scm.

(cons (channel
       (name 'domagi)
       (url "https://git.systemreboot.net/domagi/")
       (branch "main")
       (introduction
        (make-channel-introduction
         "b35f8cf1054912282dfea938c35e1c5949d2cba6"
         (openpgp-fingerprint
          "7F73 0343 F2F0 9F3C 77BF  79D3 2E25 EE8B 6180 2BB3"))))
      %default-channels)

Then run

guix time-machine -C channels.scm -- shell domagi

You will be dropped into a shell with domagi on your PATH. From there, you can run any domagi command.

Using this installation method, no persistent installation is left on your machine.

Using pip

In a new directory, create a python virtual environment and activate it.

mkdir domagi
cd domagi
python3 -m venv .venv
source .venv/bin/activate

Ensure that your system has cmake, DuckDB and the verstable.h header-only library installed. Then, install the development version of domagi using pip.

pip install git+https://git.systemreboot.net/domagi/

You can now run any domagi command in this virtual environment.