• Version 3 - 01.07.2009
• Download: tar.gz, zip

This page describes how to create a local installation of the B2G MySQL database and is intended for users with some basic knowledge in MySQL databases and general server administration tasks. If you are not able to follow the steps given here, we recommend you to ask for some help from your system administrator.

After this installation you will end up with a working DB to run Blast2GO with a DB name “b2g”, user “blast2go” and a default password “blast4it” being able to run Blast2GO nearly independent from our server. This does NOT include the graph layout generation, Fisher's Exact Test functionalities, GO-Slim reduction and other web-services which are hosted at the Blast2GO or third party server sides and you will still need to access.

B2G users should keep in mind that the B2G-DB schema can be subject of changes as consequence of the continuous efforts for improving the performance and quality of our tool. We will promptly inform users about any major change, especially concerning the DB, through the B2G mail list (http://groups.google.com/group/blast2go) and web site. In general, all information to create the B2G local database is freely available at different locations. Since all the used resources are not maintained by us, third party changes can affect these instructions. We will try to keep this as up to date as possible and are happy for receiving any feedback and bug-reports. Thanks!

Please find a detailed step-by-step description below on how to proceed. Also you might have a look at the shell script “download_and_install.sh” you can download with the zip file.

Note: For the whole installation you will need about 12 GB of free disk space and 5-6 hours if everything goes well!

1. Install a MySQL Database Server: Download and install a MySQL Database Server for example from http://dev.mysql.com/downloads or with “sudo apt-get install mysql-server” under for example Ubuntu (linux).
   
   
2. Download all necessary files (e.g. with wget <file_url>):
   • http://archive.geneontology.org/latest-full/go_<YYYYMM>-assocdb-data.gz
   • ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
   • ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz
   • ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
     
     
3. Unzip all 4 files (e.g. linux-shell> gzip -d <file>)
   
   
4. Execute the file b2g_db.sql to create a database (default name: b2g), additional tables and a public user for restricted access (select only).
   
   
5. Import the latest mysql database dump (first file downloaded in step 1) to the created database. Since the GO-DB-Dump is quite big, you should have the file local on the database server and import it directly, this speeds up the import.
   1. You unzipped the file in step 3.
   2. Execute: mysql -s -h<dbname> -u<dbuser> -p<passwd> localhost < $godbname
      • Note1: Use the “silent mode” (-s) to produce less output and to speed up the import. (On a Windows system use also (-b) to suppress the beep when errors occur.)
      • Note2: You can alternatively also first open a mysql shell and than use the command “source” to import the data.
        
        
6. Import the next two files (yet unzipped) you downloaded from NCBI with:
   • linux-shell> mysqlimport -u<user> -p<passwd> –fields-terminated-by='\t' <dbname: default=b2g> /your/path/to/gene2accession
   • linux-shell> mysqlimport -u<user> -p<passwd> –fields-terminated-by='\t' <dbname: default=b2g> /your/path/to/gene_info
     • Note: On a windows system the '\t' has to be replaced by a “\t”.
       
       
7. Important: To import the last mapping file from PIR we should use the Blast2GO application interface. First, change the db-host, name and password in the Blast2GO database configuration window under “Tools” in the main menu. Than go to the menu “Tools” and press “Import PIR mapping file”. Select the unzipped file “idmapping.tb” and wait until the import is completed. This step can take a while, please be patient.
   
   Alternatively you can download the latest blast2go4pipe distribution and start the import form the command line like e.g. this:

java -cp ./home/blast2go/b2g4pipe/blast2go.jar:./home/blast2go/b2g4pipe/ext/mysql-connector-java-3.0.11-stable-bin.jar es.blast2go.prog.util.ImportPIR idmapping.tb   localhost b2gdb dbuser dbpass

Congratulations, you are done. To test your installation, check again the new database settings in Blast2GO and click on the green little arrows in the main application window. If the green GO graphs pop up you database is working correctly.