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  • GENE-counter installation problem

    Hi!

    First time poster.

    First off, 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. 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:

    >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
    etc.

    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.

    Jonny

  • #2
    Solution

    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.

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