added options for specifying genome objects for sub get_genomic_sequence
made changes to sub genomic_sequence.  Added support for passing in dataset object to avoid database call
updated for performance by minimizing database calls through the reuse of feature_type, dataset, and genome objects
Fix for unset restricted causing parameter passing to be incorrect
add process_dups script
processing dups is now done on the job engine
Add instructions to create organism dialog
increased chromosome number limit from 100000 to 200000
updates to fix bug when comparing genomic sequence; updated link to SynSyb
updated to use new naming and directories for genomic sequence comparisons
changed naming of input blastfile to work with JEX when data is changed for genomic sequence
added parameter for handling the full filename as passed in from the URL instead of creating it
evan vixed a bug
added two debugging statements, which are commented out
added in default output to local dup files (comments).