VAT/download

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Revision as of 16:42, 8 March 2011 (view source) Lukas.habegger (Talk | contribs) (→Required Software - External) ← Older edit		Revision as of 16:44, 8 March 2011 (view source) Lukas.habegger (Talk | contribs) (→Source code) Newer edit →
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	==== Source code ====		==== Source code ====
-	A TAR ball containing the source code can be downloaded here:	+	A TAR ball containing the source code (contains BIOS - a general C library - and VAT) can be downloaded here:
	* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload		* [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload
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	==== Executables ====		==== Executables ====

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Revision as of 16:44, 8 March 2011

VAT Main Page

Contents 1 Code 1.1 Required Software - External 1.2 Download 1.2.1 Source code 1.2.2 Executables 1.2.3 License information 2 Installation 2.1 Installing the external GSL and GD libraries 2.2 Installing and configuring BIOS

Code

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Required Software - External

1. GSL - GNU Scientific Library (Required for BIOS, which is a general C 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.

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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 (contains BIOS - a general C library - and VAT) 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

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Installing the external GSL and GD libraries

In order to install VAT two external libraries must be installed first. 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 BIOS. BIOS is a general C library for manipulating strings, arrays (this library requires the GSL library).

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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.