libgwas 1.0.0

['GWAS Parser Library']

libGWAS - A GWAS Parser Library for Python

• Installation

  • Install with PIP

  • Manual Installation

  • System Requirements

  • Running Unit Tests

  • Virtual Env

  • Miniconda

• Changelog

Installation

libGWAS requires python 2.7.x as well as the following libraries:

• NumPy (version 1.7.2 or later) www.numpy.org

• SciPY (version 0.13.2 or later) www.scipy.org

libGWAS’s installation will attempt to install these required components for you, however, it requires that you have write permission to the installation directory. If you are using a shared system and lack the necessary privileges to install libraries and software yourself, you should please see one of the sections, Miniconda or virtual-env below for instructions on different options for setting up your own python environement which will exist entirely under your own control.

Installation can be done in two ways:

Install with PIP

To install using python’s package manager, pip, simply use the following command:

$ pip install libGWAS

If you have proper permission to install packages, this will attempt to download and install all dependencies along with libGWAS itself.

Manual Installation

For users who do not use pip or wish to run the bundled tests as well as have a local copy of the manuals, manual installation is almost as easy.

For users with Git installed, you can simply clone the sources using the following command:

$ git clone https://github.com/edwards-lab/libGWAS

Or you may visit the website and download the tarball directly from github: https://github.com/edwards-lab/libGWAS

Once you have downloaded the software, simply extract the contents and run the following command to install it:

$ python setup.py install

If no errors are reported, it should be installed and ready to use.

Regarding PYTHON 3 I began the process of updating the code to work with both python versions 2 and 3, however, there are some real issues with some library support of version 3 that is discouraging. So, until those have been resolved, I have no plans to invest further time toward support for python 3.

System Requirements

Because libGWAS is simply a set of classes and functions, it has no specific system requirements. However, developers using the library should be aware of the fact that some parsers, such as the pedigree_parser will require that the entire dataset be loaded into memory, regardless of the filters that are in play (i.e. positional filters, such as –from-kb and –to-kb).

Running Unit Tests

libGWAS comes with a unit test suite which can be run prior to installation. To run the tests, simply run the following command from within the root directory of the extracted archive’s contents:

$ python setup.py test

If no errors are reported, then libGWAS should run correctly on your system.

Virtual Env

Virtual ENV is a powerful too for python programmers and end users alike as it allows for users to deploy different versions of python applications without the need for root access to the machine.

Because libGWAS requires version 2.7, you’ll need to ensure that your machine’s python version is in compliance. Virtual Env basically uses the the system version of python, but creates a user owned environment wrapper allowing users to install libraries easily without administrative rights to the machine.

For a helpful introduction to VirtualEnv, please have a look at the tutorial: http://www.simononsoftware.com/virtualenv-tutorial/

Miniconda

Miniconda is a minimal version of the package manager used by the Anaconda python distribution. It makes it easy to create local installations of python with the latest versions of the common scientific libraries for users who don’t have root access to their target machines. Basically, when you use miniconda, you’ll be installing your own version of Python into a directory under your control which allows you to install anything else you need without having to submit a helpdesk ticket for administrative assistance.

Unlike pip, the folks behind the conda distributions provide binary downloads of it’s selected library components. As such, only the most popular libraries, such as pip, NumPY and SciPy, are supported by conda itself. However, these do not require compilation and may be easier to get installed than when using pip alone. I have experienced difficulty installing SciPy through pip and setup tools on our cluster here at vanderbilt due to non-standard paths for certain required components, but mini-conda always comes through.

Firstly, download and install the appropriate version of miniconda at the project website. Please be sure to choose the Python 2 version: http://conda.pydata.org/miniconda.html

While it is doing the installation, please allow it to update your PATH information. If you prefer not to always use this version of python in the future, simple tell it not to update your .bashrc file and note the instructions for loading and unloading your new python environment. Please note that even if you chose to update your .bashrc file, you will need to follow directions for loading the changes into your current shell.

Once those changes have taken effect, install setuptools and scipy: $ conda install pip scipy

Installing SciPy will also force the installation of NumPy, which is also required for running libGWAS. (setuptools includes easy_install).

Once that has been completed successfully, you should be ready to follow the standard instructions for installing libGWAS.

Changelog

libGWAS.py: 1.0.0 released

• Migrated library out from libGWAS in preparation for release of new analysis program