2 Installation

To install Vclust, you can download the pre-compiled binaries, install from PyPI and Bioconda, or compile the dependencies from source. The compilation process typically takes a few minutes.

Requirements

Vclust requires Python 3.7 or higher.

2.1. Installation from PyPI

Install Vclust from PyPI.

pip install vclust

2.2. Installation via Bioconda

Vclust is available on Bioconda (https://anaconda.org/bioconda/vclust) and can be installed with the following command:

conda install -c bioconda vclust

For detailed instructions how to set up Bioconda, please refer to the Bioconda manual.

2.3. Download precompiled binaries

If you prefer to use Vclust without installation, download prebuilt binaries from the Releases tab. Select your platform and download the tool.

2.4. Compile from source

2.4.1. Requirements

1. make
2. g++ version 11 or higher
3. cmake version 3.12 or higher

2.4.2. Default Installation

The default installation of Vclust includes all functionalities except for the Leiden clustering algorithm.

git clone --recurse-submodules https://github.com/refresh-bio/vclust
cd vclust
make -j

2.4.3. Installation with Leiden algorithm support

Vclust provides igraph's implementation of the Leiden algorithm. However, because igraph requires several external dependencies (CMake 3.18, Flex, Bison), it is not integrated with Vclust by default. To install these dependencies under Debian/Ubuntu Linux, use the following command:

sudo apt-get install cmake flex bison

Then, build Vclust with Leiden algorithm support:

git clone --recurse-submodules https://github.com/refresh-bio/vclust
cd vclust
make -j LEIDEN=true

2.5. Tests

To ensure that Vclust works as expected, you can run tests using pytest.

pytest test.py