Installation
============

There are several ways to install vConTACT3. We recommend using either
`Bioconda <https://docs.anaconda.com/free/anaconda/install/index.html>`_ /
`Mamba <https://github.com/conda-forge/miniforge>`_ or **pip**.

Install with Bioconda/Mamba (new environment):
----------------------------------------------
.. code-block:: bash

   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

.. code-block:: bash

   mamba install -c bioconda vcontact3

Install with pip:
-----------------
.. code-block:: bash

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

**This is always the latest version**

Install with requirements file:
-------------------------------
.. code-block:: bash

   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 <https://github.com/refresh-bio/vclust>`_
as well: (assuming you have already installed vConTACT3)

.. code-block:: bash

   pip install vclust

If you've installed vConTACT3 via pip, in addition to these python packages, `MMSeqs2 <https://github.com/soedinglab/MMseqs2>`_
is also required. Since MMSeqs2 is not available on PyPi, you need to install it for your system. Please follow their
`instructions <https://github.com/soedinglab/MMseqs2#installation>`_. 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 <../requirements.txt>`_.