cannot create uyploaded tracks with DBI:SQLite

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cannot create uyploaded tracks with DBI:SQLite

Jayaraman, Pushkala

Hello,

I am not able to see any of the tracks I uploaded into Gbrowse via the Upload and Share Tracks.

I installed DBD:SQLite as suggested and even changed my Gbrowse.conf file to say the following:

 

 

# If no session driver is set, then GBrowse will pick one for you.

# It will use db_file for the driver and storable for the serializer

# if available; otherwise falling back to the file driver and default serializer.

 

# Override driver guessing by setting these options

# The safest, but slowest session driver...

#session driver    = driver:file;serializer:default

#session args      = Directory /rgd/gbrowse2/tmp/sessions

 

# to use the berkeley DB driver comment out the previous

# line and uncomment these two

#session driver = driver:db_file;serializer:default

#session args   = FileName /rgd/gbrowse2/tmp/sessions.db

 

# DBI backend to use for uploaded userdata.

# The SQLite option is the easiest to use and the best tested.

# if this option is commented out, then GBrowse will

# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'

# backend.

 

# For the DBI::mysql adaptor to work, you must give the web user

# permission to create databases named userdata_% using the following

# mysql command:

#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';

# Note the backquotes around the database name, and do be sure to replace "foobar" with

# a more secure password!

 

# for SQLite

upload_db_adaptor = DBI::SQLite

 

# for Berkeleydb

#upload_db_adaptor = berkeleydb

 

# for mysql

#userdb_adaptor = DBI::mysql

#userdb_host    = localhost

#userdb_user    = rgdselect

#userdb_pass    = ju5rust5swap8udr

 

 

# Debug settings

debug                  = 1

debug_external         = 1

debug_plugins          = 1

 

# Performance settings

renderfarm             = 1

slave_timeout          = 45

global_timeout         = 60

 

I still do not see any data in my tracks.. I see the track name and the configurations..

On the server side.. I see that it creates the following folders, including a conf file:

 

\  index.SQLite  SOURCES  STATUS  upload_24422.conf

 

But I still do not see any track data.. what am I doing wrong?

 

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

 


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Re: [Gmod-gbrowse] cannot create uyploaded tracks with DBI:SQLite

Jayaraman, Pushkala

Is there a configuration I need to add somewhere else apart from the Gbrowse.conf file?

 

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: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Tuesday, August 16, 2011 10:50 AM
To: [hidden email]; [hidden email]
Subject: [Gmod-gbrowse] cannot create uyploaded tracks with DBI:SQLite

 

Hello,

I am not able to see any of the tracks I uploaded into Gbrowse via the Upload and Share Tracks.

I installed DBD:SQLite as suggested and even changed my Gbrowse.conf file to say the following:

 

 

# If no session driver is set, then GBrowse will pick one for you.

# It will use db_file for the driver and storable for the serializer

# if available; otherwise falling back to the file driver and default serializer.

 

# Override driver guessing by setting these options

# The safest, but slowest session driver...

#session driver    = driver:file;serializer:default

#session args      = Directory /rgd/gbrowse2/tmp/sessions

 

# to use the berkeley DB driver comment out the previous

# line and uncomment these two

#session driver = driver:db_file;serializer:default

#session args   = FileName /rgd/gbrowse2/tmp/sessions.db

 

# DBI backend to use for uploaded userdata.

# The SQLite option is the easiest to use and the best tested.

# if this option is commented out, then GBrowse will

# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'

# backend.

 

# For the DBI::mysql adaptor to work, you must give the web user

# permission to create databases named userdata_% using the following

# mysql command:

#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';

# Note the backquotes around the database name, and do be sure to replace "foobar" with

# a more secure password!

 

# for SQLite

upload_db_adaptor = DBI::SQLite

 

# for Berkeleydb

#upload_db_adaptor = berkeleydb

 

# for mysql

#userdb_adaptor = DBI::mysql

#userdb_host    = localhost

#userdb_user    = rgdselect

#userdb_pass    = ju5rust5swap8udr

 

 

# Debug settings

debug                  = 1

debug_external         = 1

debug_plugins          = 1

 

# Performance settings

renderfarm             = 1

slave_timeout          = 45

global_timeout         = 60

 

I still do not see any data in my tracks.. I see the track name and the configurations..

On the server side.. I see that it creates the following folders, including a conf file:

 

\  index.SQLite  SOURCES  STATUS  upload_24422.conf

 

But I still do not see any track data.. what am I doing wrong?

 

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

 


------------------------------------------------------------------------------
uberSVN's rich system and user administration capabilities and model
configuration take the hassle out of deploying and managing Subversion and
the tools developers use with it. Learn more about uberSVN and get a free
download at:  http://p.sf.net/sfu/wandisco-dev2dev

_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel