Installation¶

Recommended method (pip)¶

# (Optional) Create and activate a separate conda environment
conda create -n my-momi-env
conda activate my-momi-env

# Install non-Python-package dependencies, e.g. with conda
conda install hdf5 gsl python

# Install momi and Python dependencies with pip
pip install numpy
pip install momi

Additional notes:

Installing on macOS requires additional steps. See Installing on macOS.
Depending on your system, pip may have trouble installing some dependencies (such as numpy, msprime, pysam). In this case, you should manually install these dependencies and try again.
You can download conda from anaconda or miniconda.
If you prefer not to use conda, you can install the non-Python dependencies (hdf5, gsl) with another package manager such as apt.

Installing on macOS¶

Note: Recent versions of macOS may not work,
see #50. As an alternative, consider Installing with conda (deprecated).

Installing on macOS requires OpenMP-enabled clang, which can be installed via homebrew or conda as follows:

On homebrew, do: brew install llvm libomp.
Or if using conda, do: conda install llvm-openmp clang.

You will also need to set the environment variable CC=/path/to/clang during installation.

For example, if you installed the above dependencies using homebrew, the command to install would be:

CC=$(brew --prefix llvm)/bin/clang pip install momi

If you installed clang via conda, the command would look instead like:

CC=$(which clang) pip install momi

Installing with conda (deprecated)¶

New versions of momi are no longer released on conda. However, older versions of momi that were built for conda are still available, and may be installed with the following command:

conda install momi -c conda-forge -c bioconda -c jackkamm

Note the order of the -c flags matters, it determines the priority of each channel when installing dependencies.

Troubleshooting¶

“ModuleNotFoundError: No module named ‘momi.convolution’”¶

This is usually caused by trying to import momi when in the top-level folder of the momi2 project. In this case, Python will try to import the local, unbuilt copy of the momi subdirectory rather than the installed version.

To fix this, simply cd out of the top-level directory before importing momi.

“clang: error: unsupported option ‘-fopenmp’”¶

On macOS the system version of clang does not support OpenMP, which causes this error when building momi with pip.

To solve this, make sure you have OpenMP-enabled LLVM/clang installed, and set the environment variable CC as noted in the pip installation instructions above.

Note: it is NOT recommended to replace clang with gcc on macOS, as this can cause strange numerical errors when used with Intel MKL; for example, see https://github.com/ContinuumIO/anaconda-issues/issues/8803