2 Installation

To install Vclust, you can use precompiled binaries, install it from PyPI or Bioconda, or compile it from source.

Requirements

• Python 3.7 or higher.

2.1. Installation from PyPI

Install Vclust via PyPI:

pip install vclust

2.2. Installation via Bioconda

Install Vclust via Bioconda:

conda install -c bioconda vclust

For Bioconda setup, refer to the Bioconda manual.

2.3. Download precompiled binaries

Download prebuilt binaries from the Releases tab. Choose 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 build (without Leiden algorithm support):

The default installation of Vclust includes all functionalities except for the Leiden clustering algorithm. The compilation process typically takes a few minutes.

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

2.4.3. Build 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

2.4.4. Tests

To confirm that Vclust and all associated binaries were built correctly, you can run:

./vclust.py info

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

pytest test.py