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Installing the OBITools3

Celine Mercier edited this page 2022-04-06 22:50:43 +02:00

Table of Contents

• Install with pip
• Install with git

The OBITools3 are available to download from git and PyPI.

Install with pip

First, make sure you have installed: python3>3.6, python3-venv, python3-dev, pip, CMake

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 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>3.6, python3-venv, python3-dev, 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
	pip3 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.