1. Installation

GDSCTools is written in Python and depends on a set of established scientific libraries such as Matplotlib (visualisation) and Pandas (data manipulation) to cite just a few. We post releases on the Python repository and make use of the Python ecosystem to provide a robust software. Would you have any trouble, please see the FAQS or fill an issue/ticket on github.

1.1. Python users and developers

Releases of GDSCTools are available on Pypi so GDSCTools can be installed in a Terminal using the pip command:

pip install gdsctools

Dependencies (e.g., Pandas, Matplotlib) should be taken care of automatically.

1.2. If you are new to Python

If you are not familiar with Python, or have issues with the previous method (e.g., compilation failure), or do not have root access, we would recommend to use the Anaconda solution.

Anaconda is a free Python distribution. It includes most popular Python packages for science and data analysis. Anaconda will install the software required by GDSCTools. Since it does not require root access, it should not interfere with your system.

Please, visit the Anaconda website and follow the instructions. You may need to choose between 2 versions of Python (2.X or 3.5). GDSCTools is tested under Python 2.7 and 3.5 (as well as 3.3 and 3.4) so the version should not matter.

Once anaconda is installed, open a new Terminal (under Windows, open the Anaconda prompt) and type:

conda install numpy pandas numexpr matplotlib pandas scipy jinja2 statsmodels scikit-learn

Other dependencies and GDSCTools itself can be installed as follows:

pip install gdsctools

alternatively, if you prefer to get the source code (latest version), first obtain the source code and install manually the latest code:

# go in a working directory and type:
git clone https://github.com/CancerRxGene/gdsctools
cd gdsctools
python setup.py install

1.3. Install IPython

This is not strictly speaking required to use GDSCTools, but we strongly recommend to install IPython that provides a specialised shell for Python users. If you have installed Anaconda, just type:

conda install ipython

otherwise:

pip install ipython

1.4. You have already installed GDSCTools

If you have already installed GDSCTools and want to get the latest release, use the pip as follows:

pip install gdsctools --upgrade

If you used the source code from github, then, get the lastest source code and install again. Assuming you have installed the source code from github in github_gdsctools directory, then type:

cd github_gdsctools
git pull
python setup.py install

1.5. Testing your installation

You should now be ready to use GDSCTools. A good test is to check that the following executable is available. In a shell, type:

gdsctools_anova --test

or

gdsctools_anova --help

or for developers, start an IPython shell, and type for example:

from gdsctools import *
an = ANOVA(ic50_test)

Please, go to the next section for a Quick Start session.

1.6. Open an IPython shell

Under Windows, got to All Programs–>Anaconda –>Anaconda Prompt.

A shell will be opened where you can type ipython command.

Or alternatively, under Windows, got to All Programs–>Anaconda –>IPython

1.7. Notes for windows/mac/linux

The Anaconda method was tested successfully on the following systems: MAC, Windows 7 Pack1, Fedora 19 (Nov 2015) with version 0.16.5 of GDSCTools.

Under Windows, an error was raised due to scipy. This was fixed by typing:

conda remove scipy scikit-learn -y
conda install scipy scikit-learn -y

https://github.com/scikit-learn/scikit-learn/issues/4830