Installation

Binary install

The latest self-extracting binary for the development version of BioSimSpace can be downloaded from one of the following links:

(these are portable X86-64 binaries that should work on any Linux distribution released since ~2011, or any OS X >= 10.9[Mavericks, released 2013]. Note that they are compiled with AVX enabled, so will only work on modern (>2011) X86-64 Intel/AMD processors)

Once downloaded, the binary can be unpacked as follows on Linux:

chmod +x biosimspace_devel_latest_linux.run
./biosimspace_devel_latest_linux.run

or on OS X:

chmod +x biosimspace_devel_latest_osx.run
./biosimspace_devel_latest_osx.run

Both of these commands will let you choose where to install BioSimSpace. By default, this will be into $HOME/biosimspace.app.

For developers

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

  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_INSTALL, e.g.

BSS_SKIP_INSTALL=1 $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.