Added ability to specify database connection parameters on command line.
Added ability to specify database connection parameters on command line.

Added ability to specify one or more source names on command line, plus placeholder for doing the same for species.

Removed deprecated uses of defined()

mjg17/ensembl,danstaines/ensembl,james-monkeyshines/ensembl,james-monkeyshines/ensembl,mjg17/ensembl,danstaines/ensembl,at7/ensembl,mjg17/ensembl,at7/ensembl,muffato/ensembl,Ensembl/ensembl,muffato/ensembl,mjg17/ensembl,at7/ensembl,willmclaren/ensembl,Ensembl/ensembl,Ensembl/ensembl,willmclaren/ensembl,james-monkeyshines/ensembl,at7/ensembl,danstaines/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl,muffato/ensembl,muffato/ensembl