VAT/download
From GersteinInfo
(Difference between revisions)
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__TOC__ | __TOC__ | ||
| - | == Software == | + | == External Software == |
<center>[[#top|Top]]</center> | <center>[[#top|Top]]</center> | ||
| - | === Required | + | === Required === |
* [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (Required for BIOS, which is a general C library) | * [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library (Required for BIOS, which is a general C library) | ||
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| - | === Optional | + | === Optional === |
* [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files. | * [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files. | ||
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<center>[[#top|Top]]</center> | <center>[[#top|Top]]</center> | ||
| - | == | + | == VAT Download == |
<pre> | <pre> | ||
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| - | + | === Source code === | |
A TAR ball containing the source code (contains BIOS - a general C library - and VAT) can be downloaded here: | A TAR ball containing the source code (contains BIOS - a general C library - and VAT) can be downloaded here: | ||
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| - | + | === Executables === | |
Statically built binaries for UNIX can be found here: | Statically built binaries for UNIX can be found here: | ||
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| - | + | === License information === | |
The software package is released under the [http://creativecommons.org/licenses/by-nc/2.5/legalcode Creative Commons license (Attribution-NonCommerical)]. <br> | The software package is released under the [http://creativecommons.org/licenses/by-nc/2.5/legalcode Creative Commons license (Attribution-NonCommerical)]. <br> | ||
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| - | + | == Installation == | |
<center>[[#top|Top]]</center> | <center>[[#top|Top]]</center> | ||
| - | + | === 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 [http://www.gnu.org/software/gsl/ GNU Scientific Library] website): | 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 [http://www.gnu.org/software/gsl/ GNU Scientific Library] website): | ||
<pre> | <pre> | ||
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<center>[[#top|Top]]</center> | <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: | 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> | <pre> | ||
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<center>[[#top|Top]]</center> | <center>[[#top|Top]]</center> | ||
| - | + | ===Installing VAT=== | |
A few simple steps are required to install VAT: | A few simple steps are required to install VAT: | ||
<pre> | <pre> | ||
Revision as of 16:14, 7 April 2011
Contents |
External Software
Required
- GSL - GNU Scientific Library (Required for BIOS, which is a general C 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
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
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
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).
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.
Installing VAT
A few simple steps are required to install VAT:
$ cd /pathToVAT/ $ make
