Installation

Basic installation

To use the latest release of bamboost, install it using the python package registry.

pip install bamboost

The package requires the following packages, which pip tries to install automatically:

• h5py
• numpy
• pandas
• mpi4py

Issues with mpi4py

If you run into issues installing mpi4py, make sure that a python distribution containing the header files is installed on your system. Google this for your distribution. On Linux, a suitable package will be named python3-dev or libpython3.8-dev (insert the python version accordingly).

Parallel support for writing HDF5 files

For MPI support, h5py needs to be compiled with MPI support. To do so, you will need a local installation of the HDF5 library. If you have this, you can build h5py with MPI support by running

Install h5py with MPI support

export CC=mpicc
export HDF5_MPI="ON"
pip install --force-reinstall --no-binary=h5py h5py

Installation in editable mode

If you plan to modify the source code, you can install bamboost in editable mode. This will allow you to modify the source code and use the modified version without having to reinstall the package.

git clone git@gitlab.com:cmbm-ethz/bamboost.git
cd bamboost
pip install -e .