Perl error in MySQL and DBI

Question

I'm a student of bioinformatics and I am using the OrthoMCL tool using this command

./orthomclLoadBlast my_orthomcl/orthomcl.config my_orthomcl/similarSequence.txt

but I am getting the error

Can't connect to data source ' :mysqllocalinfile=1' because I can't work out what driver to use (it doesn't seem to contain a 'dbi:driver:' prefix and the DBI_DRIVER env var is not set) at /home/linux/Desktop/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56

DBI is already installed in my system, so why is it giving this error? How do I solve it?

Answer 1

you should use mysql for the driver:

sample:

use DBI;
$dbh = DBI->connect('dbi:mysql:DBNAME','root','password')

Answer 2

You need database drivers to be installed for the DBI module to work with your database. In this case it looks like you need to install DBD::mysql.

It is possible that OrthoMCL omits the driver name and uses just dbi::, in which case you must set the environment variable DBI_DRIVER to mysql.

The proper answer must be in the documentation for OrthoMCL. Have you read it?

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Update

Looking at the source for orthomclLoadBlast it looks like your config file is faulty. There is a chance that someone here is familiar with the utility, but you must publish orthomcl.config to stand a chance of getting any useful advice.