Error in setting up a local blast2go database

Question

[john]

Hi, I'm trying to set up a local blast2go on my workstation (Bio-linux 8). I'm following the steps found here: https://www.blast2go.com/b2gsupport/resources/35-localb2gdb

The thing is I'm having a problem importing the mapping file. I entered this on the command line

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

and got this

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

I'm getting the same error with or without the mysql connector downloaded. Any tips? Thank you.

Answer 1

[Ilona]

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! :-)

[john]

Hi thank you for your response. I asked for support in Blast2Go and apparently I'm not using the ImportIDMapping that I've also downloaded.

[Ilona]

Yes, you have to be in the folder where you downloaded your idmapping.tb file or you have to provide a path to it. Hope you already solved the issue by now! :-)