Temporary fix to solve incorrect orientation of the HG1211_PATCH until either the file contains this information or we decide to do it another way

Module associated with the Broad Magnaporthe Comparative DB; inherits fro mthe generic broad parser, Broad_GenericParser.pm

Download release version from public FTP. Also do checks for the other Ensembl modules which isn't a total failure but can trip people up

changed deprecated fetch_by_MethodLinkSpeciesSet_DnaFrag to fetch_all_by_MethodLinkSpeciesSet_DnaFrag

Added a section which does checks to make sure we have the executables available & if not then use locate to find alternatives.

first pass at helper object to be used to construct and parse common sets of command line options for misc_scripts (e.g. -dbname etc.)

Updated logic_name XrefExeonerateProtein and XrefExeonerateDNA to all lower cases to match the production database

Program is now executable and also attempts to diagnose the issues a user can face when setting up the API.