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.. index:: installation, pip, anaconda

Installation

Note

For those insterested, as from Oct 11 2017, we provide a Signularity container.

You know bioconda, then you can install GDSCTools as follows:

conda install gdsctools

Otherwise, please read this section in details.

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 troubles, please see the :ref:`faqs` or fill an issue/ticket on github.

Installation using Conda

Install conda executable

In practice, we do use Anaconda . We recommend to install conda executable via the manual installer (download <https//continuum.io/downloads>_). You may have the choice between Python 2 and 3. We recommend to choose a Python version 3.

Add conda channels

When you want to install a new package, you have to use this type of syntax:

conda install ipython

where ipython is the package you wish to install. Note that by default, conda looks on the official Anaconda website (channel). However, there are many channels available. We will use the bioconda channel. To use it, type these commands (once for all):

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Warning

it is important to add them in this order, as mentionned on bioconda webpage (https://bioconda.github.io/).

Create an environment

Once conda is installed, open a new shell. Although this is not required strictly speaking, we would recomment to create an environment dedicated to Sequana. This environment can later be removed without affecting your system or conda installation. A conda environment is nothing else than a directory and can be created as follows:

conda create --name gdsctools_env python=3.5

Then, since you may have several environments, you must activate the gdsctools environment itself:

source activate gdsctools_env

Install gdsctools via conda (bioconda)

Finally, just type:

conda install gdsctools

This should install most of the required dependencies. However, you may need to install more packages depending on the pipeline used.

Installation using pip

Python users and developers

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

pip install gdsctools

Dependencies (e.g., Pandas, Matplotlib) should be taken care of automatically. However, compilation are needed making the installation process much longer.

Installation from source

git clone https://github.com/CancerRxGene/gdsctools
cd github_gdsctools
git pull
python setup.py install

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 :ref:`quickstart` session.

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

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

Testing or Production with a Singularity container

We provide a Singularity image on https://singularity-hub.org/collections/480/ . This container contains GDSCTools software and all its dependencies. The plotting may not work in an interactive way for Mac or Windows users. The main reason being that under Mac and windows a virtualbox is used by Singularity preventing a X connection. This should be solved in the near future.

First, install singularity (http://singularity.lbl.gov/). Second, download a Sequana image. For instance, for the latest master version:

singularity pull shub://CancerRxGene/gdsctools:release_1_0_0

Do not interrupt the download (2.5Go). Once downloaded, you can use, for instance, the gdsctools_anova executable:

singularity exec gdsctools-release_1_0_0.img gdsctools_anova --help

Would you miss a dependency, just enter into the singularity container and install the missing dependencies. You will need writable permission:

sudo singularity shell -w gdsctools-release_1_0_0.img

Then, inside the container, install or fix the problem and type exit to save the container.