IMPORTANT - READ CAREFULLY:
Copyright.GenomeVISTA Copyright (c) 2012, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and Lawrence Livermore National Security. All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "GenomeVISTA (LBNL Ref CR-3197)."
NOTICE. This software was developed under funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
Prerequisites.GenomeVISTA requires the following software installed on your computer:
MySQL server v. 5.0.10 - 5.5.2.
Note: By default, the program expects that the server is running on the local machine (IP 127.0.0.1), but this can be changed at the installation time.
- MySQL client programs (only on Linux and Mac OS X).
- Perl modules: DBI, DBD-mysql, libwww-perl (only on Linux and Mac OS X).
- Java v. 1.6+.
- MySQL server v. 5.0.10 - 5.5.2.
How to install.
Download the file "install_wgv_3rd_party.jar".
Note: Third-party software required by GenomeVISTA includes a number of components with separate copyright notices and license terms. Your use of the binary and source code of these components is subject to the terms and conditions of the corresponding licenses. Some of the licenses allow only non-commercial use of the programs. The source code, copyright notices, and license terms for the third-party software are available for download here.
- Download the file "install_wgv.jar".
- Open a terminal window.
- Set environment variables JAVA_HOME or JRE_HOME to point to the Java SDK or JRE location respectively.
- Go to the directory where the downloaded jar files are located.
- Fisrt, install third-party software needed for GenomeVISTA by running "java -jar install_wgv_3rd_party.jar".
- After that, install GenomeVISTA by running "java -jar install_wgv.jar". When asked about the installation path, please enter the same directory that you specified for the third-party software. On the next screen please choose the first option - "Install".
- Set up the database using the file "setup_database.sql" located in "[INSTALL_PATH]/sql". If you do not know how to do that, you will have to ask your sysadmin for help.
- Copy the file "[INSTALL_PATH]/base/lib/libintl.8.dylib" to "/usr/local/lib" (only on Mac OS X).
- Download the file "install_wgv_3rd_party.jar".
How to use.
To start the GenomeVISTA pipeline, run:
- "[INSTALL_PATH]/scripts/start_wgv.sh" (Linux/Mac OS X)
- "[INSTALL_PATH]/scripts/start_wgv.bat" (MS Windows)
- Enter http://127.0.0.1:8765/vista-alignment/ in the web browser to access the GenomeVISTA Web application.
- To start the GenomeVISTA pipeline, run:
- Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9.
- Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole-genome alignments without a reference organism. Genome Res. 2009 Apr;19(4):682-9. Epub 2009 Jan 28.
- Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Glocal alignment: finding rearrangements during alignment. Special Issue on the Proceedings of the ISMB 2003, Bioinformatics, 19: 54i-62i.