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.

Adding in methods to retrieve repeat types from repeat_consensus. Also increased the number of types we can limit by at once

Applying a fix for when the schema patcher is run from the misc-scripts directory and now default it to the current directory if no directory is extracted from __FILE__. We also have improved the warning about missing directories

Changes to allow for a global path setting to be given as well as delegating to the meta table. Also made the data_file be able to hand back the external data adaptor

Bugfix for issue raised by Michael Nuhn from Ensembl Genomes. fetch_all_by_Transcript_list() incorrectly assigned the canonical translation ID

Pushing in a non-interactive mode. Important since some people are happy to do dry runs & then apply