Installation

The package can be installed from either bioconda, or via pip.

conda install

Our recommendation is to install cvanmf from bioconda. To do this you should have conda, or one of the reimplementations (mamba/micromamba), installed. The example below will use conda but the install commands are the same for mamba or micromamba.

To install in a new environment, run the command below, replacing {env_name} with the name you want for the environment.

conda install --name {env_name} -c bioconda -c conda-forge cvanmf

pip install

To install via pip, you will need a version of python >=3.12. Run:

pip install cvanmf

Test installation

Test the installation by running one of the commands, which should now give you a brief message

rank_select

Usage: rank_select [OPTIONS]
Try 'rank_select --help' for help.

Error: Missing option '-i' / '--input'.

Troubleshooting

Issues with gcc

Some packages which cvanmf depends upon require gcc to install, which is not available on some systems by default. If using conda/mamba you can install it in the local environment

mamba install --name cvanmf gcc

or use the system package manager for to install (e.g. sudo apt install gcc for debian based distros).

Additional installation: Jupyter

Many examples in this documentation are written as Jupyter notebooks, and this can be a convenient way to use the package. For an introduction to Jupyter Lab see here.

To install Jupyter Lab

conda install --name {env_name} jupyterlab

When installed, to launch Jupyter lab, with the cvanmf environment active, run

jupyter lab