BioCoRE - Biological Collaborative Research Environment

This step assumes that you have remote access (via an IP port) to a running, stable MySQL server. If you do not have this access, you need to install MySQL.

Create the database that BioCoRE needs

  1. Create a BioCoRE database. Start a mysql client as the root user and say: 'create database the_name_you_want;'. We would suggest something like: 'create database biocore;'. (If you don't use the name we suggest you'll need the change lines below that specify the name)
  2. You now need to create a user for MySQL (not a Unix user; rather a MySQL one). We are going to use the username "bcdbuser" (BioCore DataBase USER) (You can use any username you wish). We are also going to use a password of "USERPASS". (You need to use something more secure :)

     

    Give the MySQL user "bcdbuser" permission to do things with the biocore database: (the first three lines clean out some extraneous entries that were possibly put in during MySQL installation. After doing the delete you will probably be told that 2 rows were affected. If you aren't, your install probably didn't insert the extraneous entries and there isn't anything to worry about. Hopefully it is obvious that if you are using mysql for anything else on your system, you don't want to delete all of your mysql users.) 
    use mysql;
delete from user where User="";
flush privileges;
grant all on biocore.* to "bcdbuser" identified by "USERPASS";
    Quit MySQL with 'quit'.

  3. Unpack BioCoRE files.

     

    In the first installation step (downloading packages) you should have downloaded the BioCoRE server files from the Theoretical and Computational Biophysics website. Untar this file into a temporary directory. This will give you a a directory with a README file, a .war file, a databaseTables.txt file and some other files.

    We need to make tables for the database (and maybe populate it). We have a file in the above distribution that contains the necessary commands to create all of the tables that you need and this file is called databaseTables.txt.

    So, you need to create the database tables (initially empty) with one of the following commands:
  4. If you installed MySQL using the documentation at mysql.com, it should have installed a mysql client. You need to locate the client. It is probably already in your unix path and, if not, you will need to modify the following statement: (Note that you might need to add the -h my.machine.name option as mentioned earlier) 
    mysql -u bcdbuser -p biocore < /PATH/TO/THE/SETUP/FILE/databaseTables.txt
    When asked for a password, enter the password that you chose for the "bcdbuser".

  5. If you installed MySQL using the detailed instructions that we wrote on the previous page: 
    $DBMS_HOME/mysql/bin/mysql \
--defaults-file=$DBMS_HOME/scripts/my.cnf \
-u bcdbuser -p biocore < /PATH/TO/THE/SETUP/FILE/databaseTables.txt
    When asked for a password, enter the password that you chose for the "bcdbuser".

Next Step: Install Other Necessary Packages.
Back to the installation page

Feedback

The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.