This is the new server for Please let us know if you notice anything weird while it's getting broken in.

Migrating from GBrowse 1.X to 2.X

Revision as of 06:14, 26 August 2010 by Clements (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

This is a guide for existing users of the GBrowse 1.X series to help them migrate to version 2.0 and higher. For first-time users, please see GBrowse 2.0 HOWTO.

GBrowse 2.0 is mostly backward compatible with the 1.0 series, but there have been some changes to the layout of configuration files that make the system easier to configure and maintain. A small amount of work is needed to make your existing system work with the 2.0 series.

Apache Environment Variables

GBrowse 1.X found the location of its configuration files by consulting a hard-coded variable located in the CGI script itself. This made it hard to move the configuration files around. In contrast, GBrowse 2.0 finds its configuration directory by consulting an environment variable named GBROWSE_CONF that is set by Apache. You must add a 'SetEnv directive in the Apache configuration file in order to create this variable and pass it through. Usually this directive will be located in the "cgi-bin" <Directory> section as follows:

 <Directory /usr/lib/cgi-bin>
   SetEnv GBROWSE_CONF /etc/GBrowse2
   ... # other stuff # ...

Other environment variables that can be set in the Apache configuration file include:

Location of GBrowse's static HTML files and images in the file system (e.g. "/var/www/gbrowse2")
Location of GBrowse's static HTML files and images in URL space (e.g. "/gbrowse2")
Name of the GBrowse master configuration file located in the configuration directory, "GBrowse.conf" by default.
Colon-delimited list of directories to search for Perl modules. Useful if some modules, such as bioperl, are installed in non-standard locations.

The Build script will guide you through selecting most of these options when you run "./Build config". You can then create a suitable fragment of Apache configuration file code to cut and paste into its configuration file by running ./Build apache_config.

GBrowse.conf and Data Source Config Files

In GBrowse 1.X, each data source had its own configuration file. However, many or most of the options in each file, such as file paths, stylesheets, and header/footer options, were the same, causing config file bloat. In GBrowse 2.0, all common configuration options have been moved into a master configuration file, usually located at /etc/GBrowse2/GBrowse.conf.

GBrowse.conf contains a [GENERAL] stanza that sets such options as the location of the data-specific configuration files, static HTML, Javascript and CSS files, timeouts, session settings and global appearance settings. It also contains one or more data-source stanzas, one for each species (or genome annotation release) you want to make available for browsing. Each data-source specific stanza looks like this:

 description = This is a description
 path        = datasource.conf

The description appears in the pop-up menu that allows users to select the genome to browser. The path specifies the path to the configuration file for that data source. The Build process installs an example GBrowse.conf for you, so you can see how this is done.

Each data-source specific configuration file also has a [GENERAL] stanza. Options in this stanza supplement or override settings in GBrowse.conf. Usually there will be only a very few options in this stanza. Following this there is a [TRACK DEFAULTS] stanza that sets default options for tracks, followed by a series of [TRACK_NAME] stanzas for configuring individual tracks.

To migrate your GBrowse 1.X configuration files to 2.0, simply customize the [GENERAL] section of the new GBrowse.conf file to meet your needs, and then create a [datasource] section that points to each of your existing GBrowse 1.X config files. In most cases, these config files will work as is. Later, you may wish to consolidate redundant options that are shared among your config files in order to simplify maintenance.

Specifying Databases

In GBrowse 1.X each data source could be attached to one and only one database. In GBrowse 2.0, you can declare as many databases as you like, and attach them to one or more tracks. The syntax is simple. Somewhere in the data source configuration file (suggested: between [GENERAL] and the track stanzas) declare one or more [name:database] stanzas. For example:

  db_adaptor    = Bio::DB::SeqFeature::Store
  db_args       = -adaptor memory
                  -dir    /usr/share/databases/volvox_gb_mirror

  db_adaptor   = Bio::DB::SeqFeature::Store
  db_args      = -adaptor DBI::mysql
                 -dsn     volvox_ncRNA

This declares two databases, one named "volvox_genbank" and the other "volvox_local". You then assign these to the tracks as follows:

  database = volvox_genbank
  feature  = gene:genbank
  ... etc...

  database = volvox_ncRNA
  feature  = miRNA
  ... etc...

The default database is specified in the [GENERAL] or [TRACK DEFAULTS] section, with the latter taking precedence over the former:

 database = volvox_genbank   # this will be the default
 ... etc...

For backward compatibility, you can forego the [:database] sections entirely and just place db_adaptor and db_args options directly in the [GENERAL] and/or [TRACK] stanzas. The system will do its best to minimize the amount of redundancy and uniqueify the databases.

Specifying Rendering Slaves

GBrowse 2.0 supports rendering slaves, which are small network-based servers that receive track rendering requests from the GBrowse server and generate the text and graphics needed for a track. By judiciously spreading out the work among multiple slaves, you can speed up rendering considerably. On multiprocessor systems, there is also an advantage to having one or more rendering slaves running on the local host.

To attach a rendering slave to a track, add the remote renderer option, giving the host and port of the slave in URL format:

  feature  = gene:genbank
  remote renderer =
  ... etc...

  database = volvox_ncRNA
  feature  = miRNA
  remote renderer =

The database and remote renderer options are independent of each other, and can be mixed and matched according to your needs. See Running GBrowse 2.0 Rendering Slaves for more information on setting up renderers.