CGI/Perl Guide | Learning Center | Forums | Advertise | Login Site Search: in Perl Guide PerlGuru Forums Learning Ctr

	MAIN INDEX	SEARCH POSTS	WHO'S ONLINE	LOG IN

Home: Perl Programming Help: DBI: Perl-MySQL interface problem with GENE counter

Jonny_D New User Apr 19, 2013, 4:34 AM Post #1 of 3 (21559 views) Perl-MySQL interface problem with GENE counter Can't Post  Hi! 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. Jonny

FishMonger Veteran / Moderator Apr 19, 2013, 6:12 AM Post #2 of 3 (21554 views) Re: [Jonny_D] Perl-MySQL interface problem with GENE counter [In reply to] Can't Post 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)

Jonny_D New User Apr 19, 2013, 6:33 AM Post #3 of 3 (21550 views) Re: [FishMonger] Perl-MySQL interface problem with GENE counter [In reply to] Can't Post 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... Jonny

Announcements     PerlGuru Announcements Perl Programming Help     Frequently Asked Questions     Beginner     Intermediate     Advanced     Regular Expressions     mod_perl     DBI     Win32 Programming Help Fun With Perl     Perl Quizzes - Learn Perl the Fun Way     Perl Golf     Perl Poetry Need a Custom or Prewritten Perl Program?     I need a program that...     I Need a Programmer for Freelance Work     Throw Down The Gauntlet General Discussions     General Questions     Feedback     Tutorial/Article Suggestions for The Learning Cent     Internet Security Other Programming Languages     Javascript     PHP

Search this forum this category all forums for All words Any words Whole Phrase (options)

Powered by Gossamer Forum v.1.2.0

Web Applications & Managed Hosting Powered by Gossamer Threads
Visit our Mailing List Archives