From ac10eb8eafef0ad03e27f7fc5dbcaf48e556e581 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 20 May 2020 16:57:35 +0200 Subject: [PATCH] Update Installing the OBITools3 --- Installing-the-OBITools3.md | 35 ++++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/Installing-the-OBITools3.md b/Installing-the-OBITools3.md index ed42fc0..eea03a3 100644 --- a/Installing-the-OBITools3.md +++ b/Installing-the-OBITools3.md @@ -1,4 +1,37 @@ -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**