Bugfixes to pacify pgsql: changed a non-functional "HAVING" into a nested SELECT, and changed unsupported SUM() into COUNT(CASE … )

An important comment about UNIX sockets (without a port number) vs TCPIP sockets (with a port number).

Expose parts of pipeline_db, make them less EnsEMBL-specific, allow multiple failover initializers and use self-reference if none of them worked. Phasing out $self->o('ENV', …) expressions

Allow skipping the port number; you no longer need to define your port if you are happy with driver's default (thanks to db_conn.pl and core's DBConnection)

Registry support is now cenralised in DBAdaptor, so scripts just pass reg_* options into the constructor. Passing -reg_type allows to connect to originally non-Hive Registry entries.

Start using the new db_conn.pl script instead of building driver-specific commands and running them.

Execute individual SQL commands as well as sessions; translate some db-meta SQLite into Bash; control verbosity

Schema change: changed the data type of monitor.analysis to TEXT as per Michael Paulini's suggestion, to fit more and longer analysis names.

Allow multiple driver-dependent versions of the same patch; suggest schema patching with db_conn.pl commands.

A unified dispatching client for databases. Finds the correct database client via -url or -reg_conf/-reg_alias combination.

Give a more meaningful warning if EHIVE_ROOT_DIR is not set (probably because an external script is trying to run Hive API)

included a new -nosqlvc flag in beekeeper.pl and runWorker.pl to overcome the version restriction in non-critical cases

bugfix: propagate no_sql_schema_version_check parameter through the URLFactory/DBAdaptor loop (should be re-factored at some point)

changed the interface of balance_semaphores() : pass in $filter_analysis_id instead of $filter_analysis

tell the user whether to update the code to match the database SQL schema version, or which SQL patches to apply to the database