Gbrowse and InterMine

GBrowse is an interactive, generic, web-based genome annotation viewer created as part of the GMOD project. InterMine is able to export GFF and FASTA files suitable for importing into a GBrowse instance. Links in GBrowse can then refer to InterMine object report pages and the report pages can have links to GBrowse.

The GBrowse website has installation instructions and a tutorial. Note that BioPerl is a requirement of GBrowse.

Properties

The dbname, username and password are set in build.properties.<mine>-gbrowse. Note that due to a mis-feature these properties will need to be in build.properties.<mine> also. It's fine to have a symbolic link from build.properties.<mine> to build.properties.<mine>-gbrowse. From version 12 of FlyMine/InterMine the build.properties.<mine>-gbrowse will no longer be used and all properties should go into build.properties.<mine>. 

  project.title=FlyMine
  project.sitePrefix=/flymine
  gbrowse.database=gbrowse
  gbrowse.database.adaptor=mysql
  gbrowse.database.source=my-mine-release-1.0
  gbrowse.database.host=localhost
  gbrowse.database.user=username
  gbrowse.database.password=password
  gbrowse.database.write.user=username
  gbrowse.database.write.password=password

The gbrowse.database.source property is user visible name of the GBrowse configuration. It will appear in URLs and on the GBrowse pages. For example in FlyMine a GBrowse URL could be: 

  http://www.flymine.org/cgi-bin/gbrowse/flymine-release-11.0/?label=Genes;name=FlyMineInternalID_1090061028;width=750

In this case flymine-release-11.0 is the gbrowse.database.source. This property is also used by GBrowse to choose the configuration file to use from the gbrowse.config.directory (see below). For example if the property is set to test-mine, the file will be called test-mine.conf. See the Gbrowse documentation for information about the file.

The gbrowse.database.write.*, gbrowse.database and gbrowse.database.host properties are used by the load-gbrowse-data-mysql target. The gbrowse.database.user and gbrowse.database.password, gbrowse.database.host, gbrowse.database and gbrowse.database.source properties are used by ant install-gbrowse-conf (see below).

Creating files for GBrowse

On your local machine, in <mine>/gbrowse: 

  ant write-gff

which writes GFF and FASTA files for each chromosome to the <mine>/gbrowse/build/gbrowse/data/ directory.

This command may use more the the default memory available for Java. See the note about setting ANT_OPTS, at the bottom the Prerequisites page to increase the limit.

Loading into GBrowse

To load GFF and FASTA files into a local GBrowse schema you need:

  • a machine with GBrowse, BioPerl and MySQL installed
  • a 'gbrowse' database present in MySQL (use: mysqladmin create gbrowse)
  • set your umask to 0002 (to create files readable to all), which is needed so the the MySQL server can read the files created by the next step 
      umask 0002

Then run: 

  ant load-gbrowse-data-mysql

This loads the GFF and FASTA files into a local (MySQL) gbrowse schema.

If there are problems, run ant with the -v flag.

Installing the flymine.conf file

First make sure that these two properties to you build.properties.flymine-gbrowse: 

  gbrowse.config.directory=/etc/apache2/gbrowse.conf
  gbrowse.www.directory=/var/www/gbrowse

The directories will vary depending on where GBrowse is installed. You can also use any valid rsync path, eg. some_user@some_machine:/some/path/

Run this in <mine>/gbrowse: 

  ant install-gbrowse-conf

which command copies the a GBrowse configuration file from <mine>/gbrowse/resources/<minename>.conf into Apache's GBrowse conf directory (as configured with the gbrowse.config.directory property). While being copied the filename is changed to <source_name>.conf where <source_name> is the value of the gbrowse.database.source property.

You will need to make sure that the gbrowse.config.directory is writable by the user.

Databse host, username and password are also read from the properties and substituted into <source_name>.conf.

GBrowse uses the filename of the configuration file to create the URL to access. eg. setting gbrowse.database.source to flymine-release-3.0 gives a database that can be accessed at: http://www.flymine.org/browser/bin/gbrowse/flymine-release-3.0