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LDS / GBrowse-2.55 / htdocs / gbrowse_syn_help.html 
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<h1>Generic Synteny Browser: Example Data</h1>

These are instructions for setting up the example databases
 provided for GBrowse_syn in the GBrowse distribution.

<h2>Data Files</h2>
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.
<ul>
<li>$DATABASES/gbrowse_syn/rice/rice.gff3
<li>$DATABASES/gbrowse_syn/wild_rice/wild_rice.gff3
<li>$DATABASES/gbrowse_syn/alignments/rice.aln
</ul>


<h2>Configuration files</h2>
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.
<ul>
<li>$CONF/synteny/oryza.synconf.disabled</li>
<li>$CONF/synteny/rice_synteny.conf</li>
<li>$CONF/synteny/wild_rice_synteny.conf</li>
</ul>

<h2>Activate the Example Data Source</h2>
The joining database for the aligments currently only supports MySQL.  To install the database:
<p>
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'. 
<pre>
$ mysql -uuser -ppass 
mysql> create database rice_synteny;
Query OK, 1 row affected (0.00 sec)

mysql> grant SELECT on *.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.02 sec)

mysql> quit
Bye
</pre>

2: populate the database using the <a href="http://gmod.org/wiki/GBrowse_syn_Scripts#load_alignments_msa.pl">
 gbrowse_syn_load_alignments_msa.pl script</a> (pre-installed with GBrowse).  This will load the 
 CLUSTALW-formated alignment file above into the database.

<pre>
$ zcat DATABASES/gbrowse_syn/alignments/rice.aln.gz | gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -v -c -
</pre>

3: activate the oryza gbrwose_syn configuration file by renaming it (root-level acess required).

<pre>
# 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
</pre>


<h1> Advanced (optional) </h1>
You can speed up the image loading time by putting your species' GFF3 data into relational MySQL databases.

1: create a database for each of the GFF data files (rice.gff3 and wild_rice.gff3).
<pre>
# create a mysql database for the rice data
$ mysql -uuser -ppass  

mysql> create database rice;
Query OK, 1 row affected (0.00 sec)

mysql> create database wild_rice;
Query OK, 1 row affected (0.00 sec)

</pre>


2: populate the database using the <a 
 href="http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS">
 bp_seqfeature_load.pl</a> (pre-installed as part of BioPerl with GBrowse).  This will load the
 GFF3 data into a mySQL relational database.

<b>Note the mySQL user will need CREATE and INSERT privileges.</b>
<pre>
$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3...
Building object tree... 1.05s7s                                                                                                          
Loading bulk data into database... 0.67s
load time: 31.40s

$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3...
Building object tree... 1.15s9s                                                                                                          
Loading bulk data into database... 0.69s
load time: 31.93s

</pre>

3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny), 
changing the dsn argumant as required for each data source.

You will need to set the permissions so you can edit the files
<pre>
$ sudo chmod 644 $CONF/synteny/*
</pre>

Change:
<pre>
# from
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    $DATABASES/gbrowse_syn/rice

# to 
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn dbi:mysql:rice
                -user www-data

</pre>