Feature/cpan release 113 (#724)

* Prepare for CPAN release

- Adds file for Bio::Ensembl - this makes it easier to release to CPAN
- Adds dist.ini for Dist::Zilla
- Update cpanfile
- Add a blank line to packages, to enable Dist::Zilla to insert a
  package version

* Remove version from example code

- It's not necessary to set this explcitly. 113 is used if no version is
  given

Merge CPAN release branch (#719)

* Prepare for CPAN release

- Adds dist.ini for Dist::Zilla
- Update cpanfile
- Add a blank line to packages, to enable Dist::Zilla to insert a
  package version

* Fix travis

- Travis does not seem to have the Berkely DB headers installed

* Depend on correct bioperl, fix tests, pod

- Depend on correct bioperl version
- Fix copyright to make test suite happy
- Fix pod errors in Registry.pm

* Bioperl is now installed through the cpanfile

* Fix travis

* Fix pod errors

* CPAN Release for 112.0.0

- This is the RC for Bio::EnsEMBL version 112.0.0
- Added Changes
- Exclude some auto-discovered dependencies. They are optional and would
  prevent installation.

* CPAN Release 112.0.0

    - This is the CPAN release for Bio::EnsEMBL version 112.0.0

Merge from HEAD. Deprecating the fetch_nearest_Gene_by_Feature() meth…

…od. It is unreliable and a replacement is being developed

[ENSCORESW-757]. Cannot perform a fast query on two OR fields from th…

…e same table.

Our lookups of primary accessions and display labels with the Xref table was
flawed. Seems MySQL can only use 1 index per query and it is not possible to
create a single index that can handle querying on two columns when either
could be our matching value. Solution is to break the query into two parts
each targetting a single column. MySQL is a lot happier about this and
query times have dropped from 30 seconds on USEast to 18ms (9ms per query).

docs/README.db_portability (updated for e73).

This commit was manufactured by cvs2svn to create tag 'tag-

ensemblgenomes-20-73'.

Sprout from master 2013-08-22 09:32:14 UTC Magali Ruffier <[email protected]> 'added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively'
Cherrypick from master 2013-09-06 15:16:53 UTC Alessandro Vullo <[email protected]> 'Tests for subroutines in the Bio::EnsEMBL::Utils::IO module.':
    modules/t/io.t
    modules/t/test-genome-DBs/ontology/ontology/table.sql
    sql/patch_73_74_a.sql
    sql/patch_73_74_b.sql
    sql/patch_73_74_c.sql
    sql/patch_73_74_d.sql
    sql/patch_73_74_e.sql
    sql/patch_73_74_f.sql
Cherrypick from branch-ensembl-73 2013-08-30 09:06:03 UTC Magali Ruffier <[email protected]> 'revert changes for metacontainer support':
    misc-scripts/ontology/sql/patch_72_73_b.sql
    misc-scripts/ontology/sql/tables.sql
    modules/Bio/EnsEMBL/DBSQL/AssemblyAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
    modules/Bio/EnsEMBL/RepeatFeature.pm
    modules/Bio/EnsEMBL/Slice.pm
    modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

revert changes for metacontainer support

does not work with 73 databases as they have not been patched yet
will come back in 74

removed dnac data, tests, adaptors

removed unconventional_transcript_association

table removed from schema, modules removed, tests removed, associated calls removed

we are in the karyotype feature module, we are talking about karyotyp…

…e strand (not qtl)