Install BioSimSpace

Currently there are two options for installing BioSimSpace:

1) Download and run a docker container

docker run chryswoods/biosimspace

2) Automatic installer

For Linux and macOS there is an automatic installer script available here. This will download, install, and configure a clean BioSimSpace application. With a decent network connection, the full installation process should take around 10 minutes. After downloading the script, it can be run as follows:

chmod a+x install.sh
./install.sh

Following a successful installation, the following aliases will be set:

  • bss_python – The BioSimSpace python interpreter.
  • bss_ipython – The BioSimSpace interactive python shell.
  • bss_jupyter – The BioSimSpace Jupyter executable.
  • bss_test – Run the BioSimSpace unit tests.

(You’ll need to run source ~/.biosimspacerc or restart your shell for these to take effect.)

Note that this defaults to installing the latest stable version of BioSimSpace from the master branch. To install the development version, run:

./install.sh --branch=devel

Since the Sire binary is quite large (~700 MB), it is only re-downloaded whenever a new version is released. To force a clean install with a fresh download, run:

./install.sh --clean

3) Download and compile the source code.

BioSimSpace is built on top of the Sire molecular simulation framework. Installation requires the download and unpacking of a binary Sire application, into which BioSimSpace is installed.

First download the latest self-extracting binary release of Sire from here. Once you’ve downloaded the installer, run:

chmod a+x ./sire_XXXX_X_X.run
./sire_XXX_X_X.run

Next download the latest release of BioSimSpace from here. Alternatively, you can also keep up to date with the latest development version of BioSimSpace from GitHub:

git clone https://github.com/michellab/BioSimSpace

(Or download an archive from here.)

After unarchiving or cloning the repository, navigate to the python directory:

# Note that the directory might be named ater the version, e.g. BioSimSpace-2018.1.0
cd BioSimSpace/python

Now install BioSimSpace into your Sire application. (This assumes you chose the default installation path for Sire, i.e. $HOME/sire.app.

$HOME/sire.app/bin/python setup.py install

This will install BioSimSpace into $HOME/sire.app/lib/python3.5/site-packages, along will all of its dependencies. During the installation you can safely ignore any errors regarding mkl-random and mkl-fft. Occassionaly, conda or pip may experience network issues when installing dependencies. If this is case, simply re-run the setup.py installation above.

To test your BioSimSpace installation first run the Sire python interpreter:

$HOME/sire.app/bin/python

Now try importing BioSimSpace. If the installation was successful, you should see no errors.

import BioSimSpace

Congratulations, you are now ready to use BioSimSpace!