VAT/download

From GersteinInfo

Revision as of 16:23, 8 March 2011

Code

Required Software - External

1. GSL - GNU Scientific Library
2. BlatSuite - BLAT and a collection of utility programs. Note: these executables must be part of the PATH.
3. GD library - The GD library is used to create an image for each gene model and its associated variants.
4. Tabix - Tabix is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval (download). Note: these executables must be part of the PATH
5. VCF tools - VCF tools consists of a suite of useful modules to manipulate VCF files.

Download

Important Note
==============

THIS PACKAGE (VAT) IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Source code

A TAR ball containing the source code can be downloaded here:

• VAT-0.5.tar.gz - Initial upload

Executables

Statically built binaries for UNIX can be found here:

• VAT-0.5-UNIX.tar.gz - 64bit version

License information

The software package is released under the Creative Commons license (Attribution-NonCommerical).
For more details please refer to the Permissions Page on the Gerstein Lab webpage.

Installation

Installing the external GSL and GD libraries

In order to install VAT these external packages need to be installed first. Please, follow the instructions provided by each library. After they are installed, the first step for VAT is the installation and configuration of BIOS. BIOS is a C library of useful general definitions for manipulating strings, arrays, and parser and more related to bioinformatic analysis. It requires the GSL library, which, in most systems, can be installed with the following commands (for details, please refer to the specific instructions at the GNU Scientific Library website):

$ cd /path/to/gslSource/
$ ./configure --prefix=/path/to/installation/
$ make
$ make install

Similarly, the GD library can be installed in most systems with:

$ cd /path/to/gdSource/
$ ./configure --prefix=/path/to/installation/ --with-jpeg=/path/to/jpegLib/
$ make
$ make install

Installing and configuring BIOS

To install BIOS a few variables need to be set before compiling the library. Here is an example of the procedure on a bash shell:

$ export BIOINFOCONFDIR=/pathToBios/conf/
$ export BIOINFOGSLDIR=/pathToGsl/
$ cd /pathToBios/
$ make
$ make prod

Please refer to BIOS documentation for additional information.