Installation

There are several ways to install vConTACT3. We recommend using either Bioconda / Mamba or pip.

Install with Bioconda/Mamba (new environment):

mamba create --name vcontact3 python=3.10
mamba activate vcontact3
mamba install -c bioconda vcontact3

Install with Bioconda/Mamba (base environment):

Assuming the python in your base environment is >=3.10 and <3.12

mamba install -c bioconda vcontact3

Install with pip:

git clone https://bitbucket.org/MAVERICLab/vcontact3.git
cd vcontact3
python -m pip install .

This is always the latest version

Install with requirements file:

git clone https://bitbucket.org/MAVERICLab/vcontact3.git
cd vcontact
mamba install -c bioconda --file requirements.txt
pip install .

For users wishing to use the --exports ani option, you will need to install vclust as well: (assuming you have already installed vConTACT3)

pip install vclust

If you've installed vConTACT3 via pip, in addition to these python packages, MMSeqs2 is also required. Since MMSeqs2 is not available on PyPi, you need to install it for your system. Please follow their instructions. In the case of Apple Silicon (M1 and M2), you will need to install their OSX-universal binaries and then move that to a location in your $PATH.

These installs were verified to work on Linux x86_64. They are expected to work on Apple Intel Macs. For Apple Silicon, you may need to emulate a terminal with Rosetta support or build [failed] packages using "pip git+" and installing from source.

If you want more detailed dependencies, please check out requirements.txt.