The OBITools3 are now available to download from git and PyPI.

Install with pip

First, make sure you have installed: python3, python3-venv, pip

Then you can install the OBITools3 in a virtual environment:

  python3 -m venv obi3-env
  source obi3-env/bin/activate
  pip3 install --upgrade pip setuptools wheel Cython
  pip3 install --pre --upgrade OBITools3

If you get this error from having previously installed the deprecated alpha version:

ERROR: Cannot uninstall 'OBITools3'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

You can remove the deprecated installation with (change Python version if needed):

  rm -rf /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/OBITools3-0.0.*

  rm -rf /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/obitools3

Test the installation with:

	obi test

Once installed, you will need to be in the virtual environment to run commands (source obi3-env/bin/activate), or add the obi command to your PATH.

Install with git

First, make sure you have installed: python3, python3-venv, git, CMake

Then you can install the OBITools3 in a virtual environment:

	git clone https://git.metabarcoding.org/obitools/obitools3.git
	cd obitools3
	python3 -m venv obi3-env
	source obi3-env/bin/activate
	pip install cython
	python3 setup.py install
	source obi_completion_script.bash

And test the installation with:

	obi test

Once installed, you will need to be in the virtual environment to run commands (source obi3-env/bin/activate), or add the obi command to your PATH.