Installation

Nanomotif by default include the motif discovery, bin contamination, and include unbinned contigs modules. These modules can operate independently without the additional dependencies required for the MTase-Linker module. For details on the MTase-Linker setup, see MTase-linker installation.

Conda Environment

Using Conda for managing your Python environments, you can create a new environment and install Nanomotif as follows:

conda create -n nanomotif  python=3.12
conda activate nanomotif
conda install -c bioconda nanomotif

Local Environment

To install Nanomotif in a local Python environment:

python3 -m venv nanomotif
source nanomotif/bin/activate
pip install nanomotif

Check Installation

Once installed, the installation can be checked by running:

nanomotif check-installation

This runs a test run on a small dataset, ensuring everything works.

MTase-linker Installation

The MTase-Linker module has additional dependencies that are not automatically installed with Nanomotif. Therefore, before using this module, you must manually install these dependencies using the MTase-linker install command. The MTase-linker module requires that conda is available on your system.

nanomotif MTase-linker install

This will create a folder named ML_dependencies in your current working directory, containing the required dependencies for the MTase-linker module. You can use the --dependency_dir flag to change the installation location of the ML_dependencies folder.

usage: nanomotif MTase-linker install [-h] [-d DEPENDENCY_DIR]

optional arguments:
  -h, --help            show this help message and exit
  -d DEPENDENCY_DIR, --dependency_dir DEPENDENCY_DIR
                        Path to the directory, where dependencies should be installed. A folder named
                        ML_dependencies will be generated. Default is cwd.