VAT/download
From GersteinInfo
| Line 124: | Line 124: | ||
$ make | $ make | ||
$ make install | $ make install | ||
| + | </pre> | ||
| + | |||
| + | VAT contains a configuration file (vatConfirguration.txt), which contains a set of variables that are used by a number of different programs | ||
| + | <pre> | ||
| + | // Tabix directory | ||
| + | TABIX_DIR /path/to/tabix-0.2.3 | ||
| + | |||
| + | // CGI related variables | ||
| + | WEB_URL_CGI http://dynamic.gersteinlab.org/people/lh372/dev | ||
| + | WEB_DATA_DIR /home/lh372/public_html/VAT | ||
| + | WEB_DATA_URL http://homes.gersteinlab.org/people/lh372/VAT | ||
</pre> | </pre> | ||
Revision as of 14:44, 8 April 2011
Contents |
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 is 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/gslSource/ $ ./configure --prefix=`pwd` $ make $ make install
Similarly, the GD library can be installed on most systems with the following commands:
$ cd /path/to/gdSource/ $ ./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.
Installing and configuring 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/ $ ./configure --prefix=`pwd` $ make $ make install
Installing and configuring VAT
A few simple steps are required to install VAT:
$ cd /path/to/vat/ $ ./configure --prefix=`pwd` $ make $ make install
VAT contains a configuration file (vatConfirguration.txt), which contains a set of variables that are used by a number of different programs
// Tabix directory TABIX_DIR /path/to/tabix-0.2.3 // CGI related variables WEB_URL_CGI http://dynamic.gersteinlab.org/people/lh372/dev WEB_DATA_DIR /home/lh372/public_html/VAT WEB_DATA_URL http://homes.gersteinlab.org/people/lh372/VAT
