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
- Create a BioCoRE database. Start a mysql client as the root user
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)
- 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
use mysql; delete from user where User=""; flush privileges; grant all on biocore.* to "bcdbuser" identified by "USERPASS";Quit MySQL with 'quit'.
- Unpack BioCoRE files.
databaseTables.txtfile 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:
- 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.nameoption as mentioned earlier)
mysql -u bcdbuser -p biocore < /PATH/TO/THE/SETUP/FILE/databaseTables.txtWhen asked for a password, enter the password that you chose for the "bcdbuser".
- 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.txtWhen asked for a password, enter the password that you chose for the "bcdbuser".