Hi,
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 Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651