Generic Synteny Browser: Example Data
These are instructions for setting up the example databases
provided for GBrowse_syn in the GBrowse distribution.
Data Files
The oryza data source contains genome annotations in GFF3 flat files
for two rice species and blastz-derived whole genome aligment data between
the two species.
- $HTDOCS/databases/gbrowse_syn/rice/rice.gff3
- $HTDOCS/databases/gbrowse_syn/wild_rice/wild_rice.gff3
- $HTDOCS/databases/gbrowse_syn/alignments/rice.aln
Configuration files
Configuration files for the two species can be found at the locations
below. The oryza.synconf file is disabled pending installation of the joining database.
rice_synteny.conf and wild_rice_synteny.conf are the configuration files for the individual
species. They are already set up to use the in-memory adapter and the GFF3 flat files listed
above.
- $CONF/synteny/oryza.synconf.disabled
- $CONF/synteny/rice_synteny.conf
- $CONF/synteny/wild_rice_synteny.conf
Activate the Example Data Source
The joining database for the aligments currently only supports MySQL. To install the database:
1: create the database rice_synteny (you will need a MySQL account with CREATE and GRANT privileges).
substitute your own user name and password for 'user' and 'pass'.
$ mysql -uuser -ppass
mysql> create database rice_synteny;
Query OK, 1 row affected (0.00 sec)
mysql> grant SELECT on rice_synteny.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.02 sec)
mysql> quit
Bye
2: populate the database using the
gbrowse_syn_load_alignments_msa.pl script (pre-installed with GBrowse). This will load the
CLUSTALW-formated alignment file above into the database.
# we have to uncompress the alignment data
$ sudo gunzip $HTDOCS/databases/gbrowse_syn/alignments/rice.aln.gz
$ gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c $HTDOCS/databases/gbrowse_syn/alignments/rice.aln
3: active the oryza gbrwose_syn configuration file by renaming it (root-level acess required).
# as a sudoer
$ sudo mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf
# or as root
% mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf