Installation¶

Although it’s not possible to cover all possible ways to install PBxplore on any operating system, we try in this document to provide few guidelines regarding PBxplore setup.

Supported Platforms¶

Currently, PBxplore run with Python 2.7, 3.4, 3.5 and 3.6 on Linux and Mac OS X.

Dependencies¶

PBxplore requires the following libraries (which will be installed through ` pip`).

NumPy >= 1.6.0

NumPy is the base package for numerical computing in python.

matplotlib [1] >= 1.4.0

All ploting functions use the matplotlib package.

MDAnalysis [2] >= 0.11

We use MDAnalysis to read Gromacs molecular dynamics trajectories. Many other trajectory files are also supported, see list here.

Optionally, PBxplore can use the following packages:

Weblogo3 [3]

Weblogo3 is required to create logo from PB sequences. It has to be installed by the user.

Installing PBxplore¶

The most straightforward way is to use pip. It will also install the required dependencies:

$ pip install --user pbxplore

If none of the dependencies were previously installed, the installation process can take up to several minutes.

Note

The former command will install the PBxplore command-line scripts in:

$HOME/.local/bin on Linux.
~/Library/Python/X.Y/bin on Mac OSX, where X.Y stands for the Python version (for instance 2.7 for Python 2.7 and 3.5 for Python 3.5).

Do not forget to update your $PATH environment variable to make all PBxplore tools accessible. As an example, with the Bash shell, this gives:

$ # for Linux
$ export PATH=$PATH:$HOME/.local/bin

$ # for Mac OSX
$ export PATH=$PATH:~/Library/Python/X.Y/bin

See the documentation of pip for more information. You may also want to look at virtualenv.

Upgrading PBxplore¶

Be sure to always have the latest version of PBxplore with:

$ pip install --user --upgrade pbxplore

Testing PBxplore¶

PBxplore comes with unit tests and regression tests. It requires the package pytest. You can run the tests within Python:

import pbxplore
pbxplore.test()

Uninstalling PBxplore¶

Run the simple command:

$ pip uninstall pbxplore

PBxplore for advanced users¶

You can clone PBxplore from GitHub:

$ git clone --depth 1 https://github.com/pierrepo/PBxplore.git

Once in the PBxplore directory, we advise you to create a virtual environment:

$ pip3 install --user virtualenv
$ virtualenv -p python3 venv
$ source venv/bin/activate

You can then install the latest version of PBxplore as a Python module:

$ pip install -e .

You can also run unit tests and regression tests:

$ pip install pytest
$ pytest -v pbxplore/tests

or

$ pip install pytest
$ python setup.py test

[1]	J. D. Hunter. Matplotlib: A 2D graphics environment. Computing In Science and Engineering 9 (2007), 90-95. doi:10.1109/MCSE.2007.55

[2]	N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. doi:10.1002/jcc.21787

[3]	G. E. Crooks, G. Hon, J.-M. Chandonia, and S. E. Brenner. WebLogo: A Sequence Logo Generator. Genome Research 14: 1188–90 (2004) doi:10.1101/gr.849004