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.

Documentation

See the manual of the development version.

Contributing

Please send questions, feedback, bug reports and patches to domagi@systemreboot.net. You may also browse the archives of previous conversations. We do not accept issues or pull requests on GitHub. Thank you!

License

domagi is free software released under the terms of the GNU General Public License, either version 3 of the License, or (at your option) any later version.