Changes to externalise more items and to make the program more configurable
Changes to externalise more items and to make the program more configurable

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