testing genoogle with the bundled Aquaflex database

[Peter Woolf]

Hi there,

I'm excited about genoogle--it looks like a great piece of software
that could be really helpful! Unfortunately I'm having a hard time
testing it out because I keep getting the console error that the
databank is unknown.

I followed the posted installation process:

http://genoogle.pih.bio.br/?q=download_installation

format_db.sh works fine. But when I run the console, I could not get
any variant of the example search to work:

search Genomes_RefSeq BA000002 result_file QuerySplitQuantity=2
MaxThreadsIndexSearch=2 MaxHitsResults=20

I tried replacing Genomes_RefSeq with all kinds of Auqaflex variants,
and tried changing conf/genoogle.xml to change the data bank names,
but each time, I get the error:

2012-03-17 09:25:52,049 [Thread-2] ERROR
bio.pih.genoogle.interfaces.Console - Unknow databank aquaflex.

(or some variant depending on the databank name I'm trying)

I've created a dummy FASTA file for BA000002, so that does not seem to
be a problem.

Thoughts?

Thanks!
--Peter

[Felipe Albrecht]

Hello!

Can you show me your genoogle.xml file?

Thank you,

Felipe Albrecht

2012/3/17 Peter Woolf <pwo...@gmail.com>

[Felipe Albrecht]

By the way, 

you can execute the command  "list" in the console to see all available databases.

Felipe Albrecht

2012/3/17 Felipe Albrecht <felipe....@gmail.com>