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Perl-MySQL interface problem with GENE counter

New User

Apr 19, 2013, 4:34 AM

Views: 28156
Perl-MySQL interface problem with GENE counter


First time poster.

I'm extremely new to Perl / MySQL / Linux (Ubuntu), so there is every chance that I'm doing something ridiculous. Any help would be greatly appreciated. If i'm asking in the wrong place, sorry.

I'm trying to install a sequence database using the installDBRNASEQ.pl script which is part of a large pipeline called GENE-counter (used to analyse transcriptomic data). I have set up a MySQL database, I can log in and out without any problems, but when I run the command below from the appropriate folder location (-n, -v, variables aren't important, -i is the input file location, -d is the mysql database, -f is required by the script itself)

>perl installDBRNASEQ.pl -n Arabidopsis -v TAIR10 -i /home/jonny -d rnaseq -f

I get the following error message:

"DBI connect('rnaseq:;mysql_local_infile=1','',...) failed: Access denied for user 'root'@'localhost' (using password: NO) at /usr/local/lib/perl/GENE-counter-v0.4.4/src/installRNASEQ/../commonRNASEQ/commonRNASEQ.pm line 321.
Error: cannot connect to supplied database."

I have tried propmting for a password using derivatives of:

>perl installDBRNASEQ.pl -n Arabidopsis -v TAIR10 -i /home/jonny -d rnaseq -f -p

I'm not sure I expect that to work however as I'm running everything through Perl here. I can run another terminal window, connect to the relevant MySQL database etc., but I don't know how to specify a password and connect to the database using the above command?

Any thoughts /comments would be greatly appeciated. If anyone is willing to help I can post more info as needed.


Veteran / Moderator

Apr 19, 2013, 6:12 AM

Views: 28151
Re: [Jonny_D] Perl-MySQL interface problem with GENE counter

You need to post the installDBRNASEQ.pl script so we can see what params it accepts and how they're used.

Post it as an attachment.

(This post was edited by FishMonger on Apr 19, 2013, 6:13 AM)

New User

Apr 19, 2013, 6:33 AM

Views: 28147
Re: [FishMonger] Perl-MySQL interface problem with GENE counter

Hi FishMonger,

thanks for the reply. I think I've got to the root problem (in the last few minutes actually) which relates to a change in syntax from TYPE=MyISAM, to ENGINE=MyISAM in one of the associated Perl scripts which connects data to the mysql database. The latest MySQL update changed the syntax and I guess some Perl scripts must be lagging behind.

That was painful...