GenBank Management (GBM) ========================= Content ------- 1. File List 2. Short Install Description 3. Database Access Configuration 1. File List ------------ The following files are included in the zip'ed file: file name | file description ------------------------------------------ biojava.jar | biojava package, version 1.3.1, distributed by http://biojava.org/download/binaries/ bytecode.jar | bytecode package, version 0.92, distributed by http://biojava.org/download/binaries/ gbm.bat | start script for MS Windows gbm.conf | configuration file database access gbm.jar | central archive for the GBM application gbm.sh | start script for Unix based Computers using the bash shell jakarta-regexp.jar | downloaded from http://biojava.org/download/binaries/ mysql.jar | mysql jdbc driver package, version 3.0.8, distributed by http://www.mysql.com README | this file xerces.jar | dwnloaded from http://biojava.org/download/binaries/ if you want to replace any of the distributed files above by a newer version, please rename the new file to the names shown in the table. 2. Short Install Description ---------------------------- The program is not distributed with a installation program, so that all installation routines have to be carried out by the user. To install the program please run the folloing steps: 1. Create a new directory; we will reference it in the following as 2. Unzip the downloaded archive and copy its included files into the directory 3. If you have not installed the MySql database, please download it from http://www.mysql.com and install it please be sure that you have set the your PATH environment to /bin 4. change the directory to the /schema directory 5. start the create-db.bat / create-db.sh; if you have any problems have a look to the create-db.sql and check if the created database genedb its comprising tables are exist 6. change the directory to /program 7. eventually you have to edit the gbm.conf which contains the database access information 8. start the program by calling gbm.bat / gbm.sh 3. Database Access Configuration -------------------------------- The program needs a database to store the data of the inputed GenBank files. Generally, we use the MySQL database management system (http://www.mysql.com). But, each other relational database system can be used, too. To access the database, the program use the JDBC interface which needs a JDBC driver, the complete database url, a database user and its password. To avoid the recompilation of the program we provide a local configuration file named gbm.conf. There you can specify these four parameters. If you want to replace MySQL by another RDBMS, please also make the JDBC driver available. Please be sure that the JDBC driver, normaly located in a jar archive, is in the local directory or pointed out in systems CLASSPATH variable. By default the program prints out whenever it starts if the JDBC driver is found or not. That makes the troubleshooting easier ;-) Please let me know if you have any trouble. Have a lot of fun, Toralf (tkirsten@izbi.uni-leipzig.de)