I would like to run a Java program that accepts a VCF file from Galaxy and uses 
a JDBC connection to a postgreSQL database to do some analysis. The program 
should procude an HTML table that is then displayed in the Galaxy browser 
window. We have a local Galaxy server, and I have added my program to it using 
a configuration file. When I start the program via the framework, it just 
hangs, and "runs" forever (the command line version  finishes in a few 
seconds). I am relatively new to Galaxy and have not been able to find out how 
to trouble shoot this in the documentation. 

Some questions:
1) The tables in the postgreSQL database have been set to GRANT SELECT TO 
PUBLIC, and the Java program is connecting to the database with the name and 
password of the owner of the database. Are there any other permissions issues 
that result from the Galaxy framework?
2) Is there some way of following program execution from a shell to see what 
Galaxy is doing?
3) Any other ideas?

thanks Peter

PD Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
+4930 450566006
Mobile: 0160 93769872
Introduction to Bio-Ontologies: 
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