Apr 19, 2013, 4:34 AM
Post #1 of 3
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.