VAT/download
From GersteinInfo
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== Installation == | == Installation == | ||
| + | |||
| + | ==Installing GSL and GD libraries== | ||
| + | In order to install VAT these external packages need to be installed first . Please, follow the instruction provided by the single packages. After they are installed, the first step for VAT is the installation and configuration of [http://rnaseq.gersteinlab.org/doc/bios/ 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 [http://www.gnu.org/software/gsl/ GNU Scientific Library] website): | ||
| + | <pre> | ||
| + | $ cd /path/to/gslSource/ | ||
| + | $ ./configure --prefix=/path/to/installation/ | ||
| + | $ make | ||
| + | $ make install | ||
| + | </pre> | ||
| + | |||
| + | Similarly, the [http://www.libgd.org/Main_Page GD library] can be installed in most systems with: | ||
| + | <pre> | ||
| + | $ cd /path/to/gdSource/ | ||
| + | $ ./configure --prefix=/path/to/installation/ --with-jpeg=/path/to/jpegLib/ | ||
| + | $ make | ||
| + | $ make install | ||
| + | </pre> | ||
| + | |||
| + | <center>[[#top|Top]]</center> | ||
| + | |||
| + | ==Installing and configuring BIOS== | ||
| + | To install [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] a few variables need to be set before compiling the library. Here is an example of the procedure on a bash shell: | ||
| + | <pre> | ||
| + | $ export BIOINFOCONFDIR=/pathToBios/conf/ | ||
| + | $ export BIOINFOGSLDIR=/pathToGsl/ | ||
| + | $ cd /pathToBios/ | ||
| + | $ make | ||
| + | $ make prod | ||
| + | </pre> | ||
| + | |||
| + | Please refer to [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] documentation for additional information. | ||
| + | |||
| + | <center>[[#top|Top]]</center> | ||
Revision as of 16:20, 8 March 2011
Contents |
Code
Required Software - External
- GSL - GNU Scientific Library
- BlatSuite - BLAT and a collection of utility programs. 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.
- 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
- 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 GSL and GD libraries
In order to install VAT these external packages need to be installed first . Please, follow the instruction provided by the single packages. 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.
