Installation

There are a few options to install Mumemto, detailed below.

1. Using bioconda

Mumemto releases are available on the bioconda channel. We recommend using a fresh conda environment:

conda create -n mumemto_env python=3.12 # python 3.9 - 3.12 supported
conda activate mumemto_env

conda install -c bioconda mumemto

2. Using pip from source

The latest software is available on github, and can be installed from source. Pip will install the main mumemto executable, while also installing python dependencies for the subcommands. Again, a fresh virtual environment or conda environment is highly recommended to avoid dependency issues

# Create and activate a fresh virtual environment
python -m venv mumemto_env
source mumemto_env/bin/activate

git clone https://github.com/vshiv18/mumemto
cd mumemto
pip install .

3. Using Docker or Singularity

mumemto is available on docker and singularity.

### if using docker ###
docker pull vshiv123/mumemto:latest
docker run vshiv123/mumemto:latest -h

### if using singularity ###
singularity pull mumemto.sif docker://vshiv123/mumemto:latest
./mumemto.sif -h
 # or any subcommand, e.g ./mumemto.sif viz

For singularity, the mumemto.sif image can be used in place of the mumemto command to run subcommands. For instance, the quick start example can be run with

./mumemto.sif *.fa -o <output-prefix>
./mumemto.sif viz -i <output-prefix>

4. From source with cmake

mumemto can also be installed using cmake from source. Installing from source will create the main executable, however it will not install python dependencies (only necessary for visualization, etc.). This is particularly useful if you only want to run the multi-MUM finding algorithm.

git clone https://github.com/vshiv18/mumemto
cd mumemto

mkdir build 
cd build && cmake ..
make install

The main executable is located in build/mumemto. Optionally, you can add the build dir to your path.