Installation Guide

Instructions for installing the python library velocyto and the command line tool of the same name.

Requirements

To run velocyto you will need python >=3.6.0 (we have no plans to support python<=3.5). We recommend to use anaconda and the conda command to install dependencies limiting the use of pip to libraries not available on conda’s main channel. (pip can be used too but its dependency-managing might be less robust).

To make sure you have all the dependencies correctly installed, including libraries trickier to install, run:

conda install numpy scipy cython numba matplotlib scikit-learn h5py click

Install using PyPI

Just run:

pip install velocyto

pysam and loompy will be installed by pip as a dependencies.

Tip

velocyto 0.11 is an alpha release and it is updated often. If you installed with pip make sure you run pip install -U --no-deps velocyto often.

You can test whether the installation was successful by running velocyto --help.

To get started with velocyto you can follow our guide.

Install from source

Make sure all the requirements are satisfied, and that git is installed on your system. After doing so, run the following commands to complete the installation:

git clone https://github.com/velocyto-team/velocyto.py.git
cd velocyto.py
pip install -e .  # installs in development mode, making symlinks to the current directory

Tip

velocyto 0.11 is an alpha release, we recommend pulling in the latest bufixes and feature improvements often. Adding the -e flag installs the software in development mode, after which you can simply use git pull to update the library.

You can test whether the installation was successful by running velocyto --help.

To get started with velocyto you can follow our guide.

Install using conda

Note

This installation method is not currently available. The plan is make it available upon the 1.0 release.