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"