gbrowse_syn question

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gbrowse_syn question

Jayaraman, Pushkala
Hello,
I seem to be having problems getting the synteny viewer to work with the
sample dataset
This is the protocol I followed:
1. set up the databases in mysql. I created rice, wild_rice and
rice_synteny databases on the mysql databases I gave them all insert and
select privileges.
2. I ran the bp_seqfeature_load.pl on the rice.gff3 and the
wild_rice.gff3 files to load them into their respective databases like
this:

*bp_seqfeature_load.pl -u gbrowser -p [pass] -d
'DBI:mysql:database=wild_rice;host=forte.hmgc.mcw.edu;mysql_local_infile
=1' -c -f ../wild_rice/wild_rice.gff3

*bp_seqfeature_load.pl -u gbrowser -p [pass] -d
'DBI:mysql:database=rice;host=forte.hmgc.mcw.edu;mysql_local_infile=1'
-c -f ../rice/rice.gff3

3. I also ran the gbrowse_syn_load_alignments_msa.pl -u gbrowser -p
gbr12ws4 -d 'DBI:mysql:database=rice_synteny;host=forte.hmgc.mcw.edu' -c
-v rice.aln  

I modified the .conf files and the .synconf file to point to the mysql
database. And yet I get the "No data source" message. This is what the
apache error logs mention..


[Tue Jun 01 14:10:26 2010] [error] [client 141.106.161.52] [Tue Jun  1
14:10:26 2010] gbrowse_syn: Use of uninitialized value in concatenation
(.) or string at /usr/local/apache2
/cgi-bin/gbrowse_syn line 9, <DATA> line 192.


Where have I gone wrong?
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu

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