Installation

Required packages in python: numpy>=1.9.0, scipy>=1.0, matplotlib

Environment: we only tested Vireo in Python 3 environment, so if it fails in Python 2, please try it in Python 3 before reporting the issue.

We recommend using Anaconda distribute to set up the environment. It not only includes all dependent packages, but also provides a user controlled environment, namely, you will have the root permission for this distribution, including installation of any package.

Easy install from PyPI

You can install Vireo simply via PyPI in terminal (suggested), or upgrade by adding --upgrade as follows:

pip install vireoSNP

pip install --upgrade --no-deps vireoSNP

Install from source code

Alternatively, you can download the source code from GitHub (for the latest version) and run python setup in terminal:

wget https://github.com/huangyh09/vireo/archive/master.zip
unzip master.zip
cd vireo-master

python setup.py install

You can also use the following shortcut

pip install -U git+https://github.com/single-cell-genetics/vireo

In any case, if had the permission error for installation as you are not root, add --user.

Quick check

In order to test the installation, you could type vireo in terminal. If successfully installed, you will see the following output.

Welcome to vireoSNP v0.1.1!

use -h or --help for help on argument.

If installation is sucessful, but can’t run it (e.g., message below), then check whether the directory which contains the executable binary file is added to PATH environment.

vireo: command not found

If using Anaconda, the executable vireo is located in $anaconda3/bin/vireo. If not using Anaconda, it is usually located in directory ~/.local/bin. You could add the path into PATH environment variable, by write the following line into .profile or .bashrc file.

export PATH="~/.local/bin:$PATH"