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New version of GAMES (V1.3) for annotation and interpretation of variant from NGS m_elena_bioinfo Bioinformatics 0 05-25-2011 09:12 AM
GAMES software - NEW RELEASE V1.2 m_elena_bioinfo Bioinformatics 0 02-21-2011 09:19 AM

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Old 11-02-2010, 11:05 AM   #1
johnny
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I'm currently giving GAMES a try. Although I'm totally new to perl, I managed to get the Bioanalysis done. But now for the Annotation process, could someone please explain me in a bit more detail how one should proceed with the DB connection before one can use the Annotation.

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Old 11-16-2010, 05:34 AM   #2
johnny
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Okay, now I give some more detailed information, maybe someone can help me then.

What I get when running the Annotation part is:


Useless use of array element in void context at GAMES_annotation_NCBI36hg18.pl line 1759.

DBD::mysql initialisation failed: Can't locate object method "driver" via package "DBD::mysql" at /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level/DBI.pm line 787.

Perhaps the capitalisation of DBD 'mysql' isn't right. at GAMES_annotation_NCBI36hg18.pl line 34

------------------------

The GAMES-tutorial file saysBI->connect("DBI:mysql:$database:$hostname:$port", $username, $password)
You have to set username and password for database connection by DBI.

I think this is the problem. How can I do this ?

Last edited by johnny; 11-16-2010 at 05:43 AM.
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Old 11-16-2010, 05:56 AM   #3
drio
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Try to install the mysql-dbi module. It seems missing.
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Old 11-16-2010, 08:03 AM   #4
johnny
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perldoc DBI and perldoc DBD shows me that it is installed, but

perldoc -l DBI shows me:

/Library/Perl/5.10.0/darwin-thread-multi-2level/DBI.pm

and perldoc -l DBD::mysql

/Library/Perl/Updates/5.10.0/DBD/mysql.pm

Could this be a problem ?
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Old 11-16-2010, 08:30 AM   #5
johnny
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I think the problem is in the GAMES script. Here is the part that is supposed to be changed to the users settings. Do I have to set up a new mysql database first ?

######## DATABASE CONNECTION ########
######## REMEMBER TO SET DATABASE PATH, USERNAME & PWD FOR DBI CONNECTIONS ######

my $database = "set_db_path";
my $data_source = "DBI:mysql:$database";
my $username = "set_username";
my $password = "set_pwd";
my $hostname = "localhost";
my ($dbh,$dbh1);
my ($sth,$sth1);
my $port =3306;
my $j;
my $i;

$dbh = DBI->connect("DBI:mysql:$database:$hostname:$port", $username, $password)
or die "Can't connect to $data_source: $dbh->errstr\n";

########## GETOPT #####################
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Old 11-22-2010, 07:54 AM   #6
m_elena_bioinfo
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Hi Johnny,
I'm Maria Elena, the developer of GAMES. I read your problems with the installation of GAMES.
it seems there might be a problem with mysql perl modules installation.
Nevertheless, you need to create a db with mysql (you can install the phpmyadmin web gui, most linux installations have a package for it, if you feel uncomfortable with command lines).

DB name can be as you wish (mygames can be ok for example).

anything like the following:

my $database = "mygames";
my $data_source = "DBI:mysql:$database";
my $username = "bioinformaticianfrommars";
my $password = "alienicus";

the password and the user need to be added to the mysql privileges:
unix> mysql -u root -p
(here you will be asked the password)

mysql> create database mygames;
mysql> GRANT ALL PRIVILEGES
ON my_database.*
TO 'bioinformaticianfrommars@'localhost'
IDENTIFIED BY 'alienicus'
WITH GRANT OPTION;

mysql> FLUSH PRIVILEGES;

If you have any problems, feel free to contact me!
Bye,
ME
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