Installation

Conda install

The easiest way to install BioSimSpace is using our conda channel. BioSimSpace is built using dependencies from conda-forge, so please ensure that the channel takes strict priority. We recommend using Miniforge.

To create a new environment:

conda create -n biosimspace -c conda-forge -c michellab biosimspace
conda activate biosimspace

To install the latest development version you can use:

conda create -n biosimspace-dev -c conda-forge -c michellab/label/dev biosimspace
conda activate biosimspace-dev

When updating the development version it is generally advised to update Sire at the same time:

conda update -c conda-forge -c michellab/label/dev biosimspace sire

If you plan on using BioSimSpace interactively via Jupyter, then you might also need to enable the required notebook extensions within your Conda environment:

jupyter-nbextension enable nglview --py --sys-prefix

Unless you add the required channels to your Conda configuration, then you’ll need to add them when updating, e.g., for the development package:

conda update -c conda-forge -c michellab/label/dev biosimspace

If you find that Conda is particularly slow to install or upgrade BioSimSpace, then we advise using mamba:

conda install -c conda-forge mamba

You can then replace all conda commands with mamba, e.g.:

mamba create -n biosimspace -c conda-forge -c michellab biosimspace

Binary install

Prior to the 2022.1.0 release we provided a self-extracting binary install of BioSimSpace. Please visit our binaries page if you wish to download any of these.

For developers

The following documents a full installation of BioSimSpace from source. Before starting, you’ll need a working Git installation.

  1. BioSimSpace is built on top of the Sire molecular simulation framework. To download and install Sire:

git clone https://github.com/michellab/Sire
cd Sire
./compile_sire.sh

Assuming the default installation path, this will install Sire into $HOME/sire.app.

(Note that the installation is slow and can take in excess of an hour.)

  1. Next you will need to download BioSimSpace and install it into your Sire application. (The following assumes the default Sire installation path.)

git clone https://github.com/michellab/BioSimSpace
cd BioSimSpace/python
$HOME/sire.app/bin/python setup.py install

Once finished, you can test the installation by running:

$HOME/sire.app/bin/ipython

Then try importing the BioSimSpace package:

import BioSimSpace as BSS

When developing you may not wish to continually re-install BioSimSpace and its associated dependencies. To avoid this, you can either make use of PYTHONPATH, e.g.

PYTHONPATH=$HOME/Code/BioSimSpace/python $HOME/sire.app/bin/python script.py

or use the develop argument when running the setup.py script, i.e.

PYTHONPATH=$HOME/sire.app/bin/python setup.py develop

You can also skip installation of external dependencies by setting the environment variable BSS_SKIP_DEPENDENCIES, e.g.

BSS_SKIP_DEPENDENCIES=True $HOME/sire.app/bin/python setup.py install

Common issues

  • If you experience problems with Matplotlib when importing BioSimSpace on macOS, e.g.

RuntimeError**: Python is not installed as a framework.

simply add the following to ~/.matplotlib/matplotlibrc

backend: TkAgg

Note that plotting functionality will be disabled if you are using BioSimSpace on a remote server without X forwarding.

  • If you experience problems with Jupyter permissions, try removing $HOME/.jupyter or $HOME/.local/share/jupyter

External dependencies

Several additional packages are required for full access to all of BioSimSpace’s functionality. Please download and install these packages according to their recommended installation instructions.

For Amber / AmberTools, we also recommend adding ${AMBERHOME}/bin to your PATH to ensure that its binaries are visible to third-party libraries, such as openff-toolkit.

Please visit our compatibility page to see which versions of the external dependencies BioSimSpace has currently been tested against.