VAT/download
From GersteinInfo
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=== Required === | === Required === | ||
| - | * [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library ( | + | * [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (version-1.14; required for libBIOS, which is a general C library) |
* [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH. | * [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH. | ||
| - | * [http://www.libgd.org/Main_Page GD library] - The GD library is used to create an image for each gene model and its associated variants (required by VAT). | + | * [http://www.libgd.org/Main_Page 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). |
* [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). These tools are utilized by VAT, Note: these executables must be part of the PATH | * [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). These tools are utilized by VAT, Note: these executables must be part of the PATH | ||
| Line 88: | Line 88: | ||
<pre> | <pre> | ||
| - | + | export CPPFLAGS="-I/net/gerstein/lh372/SOFT/gsl-1.14/include -I/net/gerstein/lh372/SOFT/libbios/include -I/net/gerstein/lh372/SOFT/gd-2.0.35/include" | |
| + | export LDFLAGS="-L/net/gerstein/lh372/SOFT/gsl-1.14/lib -L/net/gerstein/lh372/SOFT/libbios/lib -L/net/gerstein/lh372/SOFT/gd-2.0.35/lib" | ||
</pre> | </pre> | ||
Revision as of 14:15, 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=/path/to/installation/ $ make $ make install
Similarly, the GD library can be installed on most systems with the following commands:
$ cd /path/to/gdSource/ $ ./configure --prefix=/path/to/installation/ --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
export CPPFLAGS="-I/net/gerstein/lh372/SOFT/gsl-1.14/include -I/net/gerstein/lh372/SOFT/libbios/include -I/net/gerstein/lh372/SOFT/gd-2.0.35/include" export LDFLAGS="-L/net/gerstein/lh372/SOFT/gsl-1.14/lib -L/net/gerstein/lh372/SOFT/libbios/lib -L/net/gerstein/lh372/SOFT/gd-2.0.35/lib"
Please refer to BIOS documentation for additional information.
Installing VAT
A few simple steps are required to install VAT:
