gbrowse_syn::: BI connect('rice_synteny', 'root', ...) failed: Access denied for user 'root'@'localhost' (using password: YES)

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gbrowse_syn::: BI connect('rice_synteny', 'root', ...) failed: Access denied for user 'root'@'localhost' (using password: YES)

rashid kazmi

Hi


I was running tutorial for gbrowse_syn (http://gmod.org/wiki/GBrowse_syn_Tutorial) and I got stuck there. Could some one help please. Desperately need it. Any help would be much appreciated.


Thanks


ras@kazmi:~$ mysql -u root -p

Enter password:

Welcome to the MySQL monitor. Commands end with ; or \g.

Your MySQL connection id is 46

Server version: 5.1.41-3ubuntu12.3 (Ubuntu)

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.


mysql> GRANT SELECT on *.* TO 'www-data'@'localhost';

Query OK, 0 rows affected (0.07 sec)

mysql> quit

Bye


I followed all the steps and they were ok till here when i tried to run this script to populate the database;


ras@kazmi:~$ gbrowse_syn_load_alignments_msa.pl -u root -p gmodamericas2010 -d rice_synteny -c -v rice.aln

DBI connect('rice_synteny','root',...) failed: Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228

Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228.


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Re: gbrowse_syn::: BI connect('rice_synteny', 'root', ...) failed: Access denied for user 'root'@'localhost' (usingpassword: YES)

Jayaraman, Pushkala

Is your database username and password also “gmod” and “gmodamericas2010” ?

If yes,

Send your configuration file..

The .synconf file

I think you haven’t written your arguments right. I came across the same errors..

 

This is how yoru synconf should look like:

 

 

[GENERAL]

description =  BLASTZ alignments for Oryza sativa

 

#the synteny database

join = dbi:mysql:database=rice_synteny;host=YOURHOST;user=USER;password=PASSWORD

 

# This option maps the relationship between the species data sources, names and descriptions

# The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.

# This value is also used in two other places in the gbrowse_syn configuration:

# the species name in the "examples" directive and the species name in the .aln file

# The value for "conf. file" is the basename of the corresponding gbrowse .conf files.

# This value is also used to identify the species configuration stanzas at the bottom of the configuration file.

 

#                 name          conf. file            Description

source_map =      rice          rice_synteny          "Domesic Rice (O. sativa)"

                  wild_rice     wild_rice_synteny     "Wild Rice"

 

tmpimages     = /tmp

imagewidth    = 800

stylesheet    = /gbrowse2/css/gbrowse_solid.css

cache time    = 0

 

 

config_extension = conf

 

# example searches to display

examples = rice 3:16050173..16064974

           wild_rice 3:1..400000

 

zoom levels = 5000 10000 25000 50000 100000 200000 400000

 

# species-specific databases

[rice_synteny]

tracks    = EG

color     = blue

 

[wild_rice_synteny]

tracks    = EG

color     = red

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: rashid kazmi [mailto:[hidden email]]
Sent: Tuesday, June 22, 2010 6:56 PM
To: [hidden email]
Subject: [Gmod-gbrowse] gbrowse_syn::: BI connect('rice_synteny', 'root',...) failed: Access denied for user 'root'@'localhost' (usingpassword: YES)

 

Hi

 

I was running tutorial for gbrowse_syn (http://gmod.org/wiki/GBrowse_syn_Tutorial) and I got stuck there. Could some one help please. Desperately need it. Any help would be much appreciated.

 

Thanks

 

ras@kazmi:~$ mysql -u root -p

Enter password:

Welcome to the MySQL monitor. Commands end with ; or \g.

Your MySQL connection id is 46

Server version: 5.1.41-3ubuntu12.3 (Ubuntu)

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

 

mysql> GRANT SELECT on *.* TO 'www-data'@'localhost';

Query OK, 0 rows affected (0.07 sec)

mysql> quit

Bye

 

I followed all the steps and they were ok till here when i tried to run this script to populate the database;

 

ras@kazmi:~$ gbrowse_syn_load_alignments_msa.pl -u root -p gmodamericas2010 -d rice_synteny -c -v rice.aln

DBI connect('rice_synteny','root',...) failed: Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228

Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228.


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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: gbrowse_syn::: BI connect('rice_synteny', 'root', ...) failed: Access denied for user 'root'@'localhost' (usingpassword: YES)

Jayaraman, Pushkala

Sure Rashid,

I’m glad it worked..

J

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: rashid kazmi [mailto:[hidden email]]
Sent: Tuesday, June 22, 2010 8:45 PM
To: Jayaraman, Pushkala
Subject: Re: [Gmod-gbrowse] gbrowse_syn::: BI connect('rice_synteny', 'root',...) failed: Access denied for user 'root'@'localhost' (usingpassword: YES)

 

Hi Pushkala

On 23 June 2010 02:00, Jayaraman, Pushkala <[hidden email]> wrote:

Is your database username and password also “gmod” and “gmodamericas2010” ?

If yes,

Send your configuration file..

The .synconf file

I think you haven’t written your arguments right. I came across the same errors..

 

This is how yoru synconf should look like:

 

 

[GENERAL]

description =  BLASTZ alignments for Oryza sativa

 

#the synteny database

join = dbi:mysql:database=rice_synteny;host=YOURHOST;user=USER;password=PASSWORD

 

# This option maps the relationship between the species data sources, names and descriptions

# The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.

# This value is also used in two other places in the gbrowse_syn configuration:

# the species name in the "examples" directive and the species name in the .aln file

# The value for "conf. file" is the basename of the corresponding gbrowse .conf files.

# This value is also used to identify the species configuration stanzas at the bottom of the configuration file.

 

#                 name          conf. file            Description

source_map =      rice          rice_synteny          "Domesic Rice (O. sativa)"

                  wild_rice     wild_rice_synteny     "Wild Rice"

 

tmpimages     = /tmp

imagewidth    = 800

stylesheet    = /gbrowse2/css/gbrowse_solid.css

cache time    = 0

 

 

config_extension = conf

 

# example searches to display

examples = rice 3:16050173..16064974

           wild_rice 3:1..400000

 

zoom levels = 5000 10000 25000 50000 100000 200000 400000

 

# species-specific databases

[rice_synteny]

tracks    = EG

color     = blue

 

[wild_rice_synteny]

tracks    = EG

color     = red

Hi Pushkala


Thanks very much indeed !!! Much appreciated for generous offer but your advice worked and I just finished my tutorial successfully :) I am relieved.so probably I don't have to send you config files.

Maybe I will disturb you some other time.

You have nice day (I assume its day time in US not like europe its 2pm)

 Regards,
Rashid

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: rashid kazmi [mailto:[hidden email]]
Sent: Tuesday, June 22, 2010 6:56 PM
To: [hidden email]
Subject: [Gmod-gbrowse] gbrowse_syn::: BI connect('rice_synteny', 'root',...) failed: Access denied for user 'root'@'localhost' (usingpassword: YES)

 

Hi

 

I was running tutorial for gbrowse_syn (http://gmod.org/wiki/GBrowse_syn_Tutorial) and I got stuck there. Could some one help please. Desperately need it. Any help would be much appreciated.

 

Thanks

 

ras@kazmi:~$ mysql -u root -p

Enter password:

Welcome to the MySQL monitor. Commands end with ; or \g.

Your MySQL connection id is 46

Server version: 5.1.41-3ubuntu12.3 (Ubuntu)

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

 

mysql> GRANT SELECT on *.* TO 'www-data'@'localhost';

Query OK, 0 rows affected (0.07 sec)

mysql> quit

Bye

 

I followed all the steps and they were ok till here when i tried to run this script to populate the database;

 

ras@kazmi:~$ gbrowse_syn_load_alignments_msa.pl -u root -p gmodamericas2010 -d rice_synteny -c -v rice.aln

DBI connect('rice_synteny','root',...) failed: Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228

Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/bin/gbrowse_syn_load_alignments_msa.pl line 228.

 


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse