VAT/download

From GersteinInfo

Revision as of 16:59, 8 April 2011

External Software

Required

• GSL - GNU Scientific Library (version-1.14; required for libBIOS, which is a general C library).
• BlatSuite - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH.
• GD library - The GD library is used to create an image for each gene model and its associated variants (version-2.0.35; required by VAT).
• Tabix - Tabix (version-0.2.3) is a generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval (download). These tools are utilized by VAT. Note: these executables must be part of the PATH.

Optional

• VCF tools - VCF tools consists of a suite of useful modules to manipulate VCF files.

VAT 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

VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:

• libBIOS-1.1.0.tar.gz
• 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

Installation of the external GSL and GD libraries

In order to install VAT two external libraries must be installed first. The libBIOS library depends on GSL, wheres VAT makes use of the GD library. Please follow the instructions provided by each package. The GSL library can be installed on most systems using the following commands (for details, please refer to the specific instructions at the GNU Scientific Library website):

$ cd /path/to/gsl-1.14/
$ ./configure --prefix=`pwd`
$ make
$ make install

Similarly, the GD library can be installed on most systems with the following commands:

$ cd /path/to/gd-2.0.35/
$ ./configure --prefix=`pwd` --with-jpeg=/path/to/jpegLib/
$ make
$ make install

After they are installed, the first step to install VAT is the installation and configuration of libBIOS.

Installation and Configuration of libBIOS

Depending on where the three libraries (GSL, libBIOS, and GD) are installed, the following variables need to be set:

export CPPFLAGS="-I/path/to/gsl-1.14/include -I/path/to/libbios/include -I/path/to/gd-2.0.35/include"
export LDFLAGS="-L/path/to/gsl-1.14/lib -L/path/to/libbios/lib -L/path/to/gd-2.0.35/lib"

libBIOS can be installed on most systems with the following commands:

$ cd /path/to/libbios-x.x.x/
$ ./configure --prefix=`pwd` 
$ make
$ make install

Installation and Configuration of VAT

A few simple steps are required to install VAT:

$ cd /path/to/vat-x.x.x/
$ ./configure --prefix=`pwd` 
$ make
$ make install

VAT contains a configuration file (vatConfirgurationTemplate.txt), which contains a set of variables that are used by a number of different programs. The name/value pairs are space or tab-delimited. Empty lines are lines starting with '//' are ignored.

// ===============================================================================
// REQUIRED
// ===============================================================================

// Tabix directory (includes both tabix and bgzip)
TABIX_DIR /path/to/tabix-0.2.3


// ===============================================================================
// OPTIONAL (required only for CGIs)
// ===============================================================================

// CGI base URL (where the CGIs are located)
WEB_URL_CGI http://webserver.org/path

// Path to the web data directory where the preprocessed files are stored
WEB_DATA_DIR /path/to/public_html/path/to/VAT
// URL to preprocessed files
WEB_DATA_URL http://webserver.org/path/to/VAT

This file has be configured properly by filling in the required information. Afterwords the following environment variable has to be set:

VAT_CONFIG_FILE=/pathTo/vat/vatConfirgurationTemplate.txt

The example workflow shows how to set up the web server.

Download of preprocessed annotation sets

The following annotation sets are derived from the GENCODE:

• GENCODE version 3b (hg18) - includes coding sequence (CDS) elements where the both the gene_type and transcript_type are protein_coding
  • gencode3b.interval - Interval file with transcript coordinates
  • gencode3b.fa - FASTA file with transcript sequences (introns are removed; sequence with respect to the '+' strand)
• GENCODE version 3c (hg19) - includes coding sequence (CDS) elements where the both the gene_type and transcript_type are protein_coding
  • gencode3c.interval - Interval file with transcript coordinates
  • gencode3c.fa - FASTA file with transcript sequences (introns are removed; sequence with respect to the '+' strand)