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
- 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
(Note that the installation is slow and can take in excess of an hour.)
- 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 $HOME/sire.app/bin/python setup.py install
Once finished, you can test the installation by running:
Then try importing the BioSimSpace package:
import BioSimSpace as BSS
When developing you may not wish to continually re-install BioSimSpace and its
associated dependencies. To avoid this, you can either make use of
PYTHONPATH=$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
BSS_SKIP_INSTALL=1 $HOME/sire.app/bin/python setup.py install
- 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
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,
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.