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Update Installing the OBITools3

Celine Mercier
2020-05-20 16:57:35 +02:00
parent 6717f521bf
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Installing-the-OBITools3.md

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The OBITools3 are now available to download from git, and will soon be on Nix ([pull request](https://github.com/NixOS/nixpkgs/pull/69644)).
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**