GBrowse: Difference between revisions

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GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. It requires a web interface to display. GBrowse has been installed on [[Cedar]]. The web address of the installation is https://gateway.cedar.computecanada.ca.

The Cedar installation differs in some ways from the standard GBrowse setup described at the official website: http://gmod.org/wiki/GBrowse, particularly with regard to authentication and authorization.

In order for GBrowse to be able to access your files and directories, Compute Canada (CC) staff will create a shared account for each research group that requests access to GBrowse. While using GBrowse, any member of a research group can read GBrowse config files and input files belonging to any other member of that group. If you wish to use GBrowse, the Principal Investigator (PI) of your group must agree to this change from the usual file security practices. Have the PI write to support@computecanada.ca indicating that they want a GBrowse account to be created for the group, and that they understand the implications of the shared account.

You must also have a database account on Cedar. If you already have one, please give the name of the database in your email. If you do not already have a database account, please read [[Database servers]] carefully and answer the questions given there for setting up a database.

Since Gbrowse needs to be able to read config files of all users within a group, place your GBrowse config files in the following directory:

where <code>GROUPID</code> is your group id and <code>USERNAME</code> is the your user name. We will create a symbolic link from <code>${HOME}/gbrowse/conf</code> to this directory for your convenience. Files in this directory should be readable by all members of the group, so please do not change the group permission of files in this directory.

If you use MySQL, you need the following in your GBrowse config files:

  db_adaptor    =    Bio::DB::SeqFeature::Store

  db_args      =    -adaptor DBI::mysql

  -dsn DATABASE;mysql_read_default_file=/home/SHARED/.my.cnf

where <code>DATABASE</code> is the name of your database and <code>SHARED</code> is the shared-account. The <code>.my.cnf</code> file is a text file that is created by CC staff. It contains information required for the shared account to make a connection to MySQL.  

If you decide to use Postgres you need the following in your GBrowse config files:

  db_adaptor    = Bio::DB::SeqFeature::Store

  db_args      =  -adaptor DBI::Pg

where <code>DATABASE</code> is the name of your database.

GBrowse is able to read <code>.bam</code> files directly. You do not need to upload them to the database in order to display them. If you want GBrowse to read these .bam files:

* Files need to be copied to your <code>/project</code> directory and they should be readable by the group.  

* Edit your config file to specify the path to the <code>.bam</code> file. Here is an example:

  db_adaptor        = Bio::DB::Sam

  db_args          = -bam /project/GROUPID/USERNAME/gbrowse_bam_files/example_file.bam

  search options    = default

This can be done using BioPerl. Here are commands that need to be run.  

  bp_seqfeature_load.pl -c –d DATABASE:mysql_read_default_file=/home/USERNAME/.my.cnf \

     example_genomic_sequence.fa header_file

In this example DATABASE is the name of your database and <code>example_genomic_sequence.fa</code> is the [https://en.wikipedia.org/wiki/FASTA_format fasta file] containing the entire genome that you want to visualize with GBrowse. <code>header_file</code> contains details about the length of the chromosomes. Here is an example of a header file:

<pre>

##sequence-region I 1 15072434

</pre>

We remind you that the above commands should be run via the [[Running jobs|job scheduler]]. Do not run these on the head node!

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