Hi John,

I'm not a bioinformatician, just trying to learn bioinformatics from scratch, but I just set up the local blast2go on our workstation in the lab (also with Biolinux 8 system). I did not find the original description from blast2go website very much detailed, but I followed these two websites :

https://groups.google.com/forum/#!msg/Blast2GO/QJhDrAb98o4/jMzPc92HxH4J

http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/blast2godb.htm

and it helped me a lot with setting up the local blast2go database!

I think it is quite important this part :

By default mysql is configured to not allow import from local files for security reason, so the next two steps would generate an error. To allow this you need to edit my.cnf. First, stop the mysql server:

sudo service mysql stop

Then edit my.cnf:

cd /etc/mysql
sudo gedit my.cnf

In the editor, add the line

local-infile = 1

to the sections [client] and [mysqld]. Save. Restart mysql:

sudo service mysql start

And then you might be missing a colon in your command after mysql-connector-java-5.0.8-bin.jar

I used this command

java -cp .:mysql-connector-java-5.0.8-bin.jar: ImportIdMapping idmapping.tb localhost b2gdb blast2go blast4it

and it seemed to work!

I hope this will be of some help to you! :-)