changed to varchar(255) (but dropped joining to analysis_data table)
If modules need more than 255 characters of input_id
they can pass the anaysis_data_id via the varchar(255) : example {adid=>365902}

workers can change batch_size as they run.

1) input_id is the command
2) input_id is formated like '{did=>123}'
  where did is short hand for analysis_data_id and the real command
  is stored in the analysis_data table

All STDOUT and STDERR from the command are autoamtically captured and redirected
to files (locations stored in analysis_job_file table).
Very simple idea, but might prove useful.

all parts of the Hive system.  Allows one to have a single use/include
use Bio::EnsEMBL::Hive;

Use instead DataflowRule and DataflowRuleAdaptor

on all anlyses, not just the ones with entries in the analysis_job table.
New logic is also faster.

logic as -loop option, but returns right away). Also modified checkk_for_dead
to take into account jobs with 'EXIT' status.

table.  Doing join on analysis_job.input_analysis_data_id=analysis_data.analysis_data_id
gives same performance as having analysis_job.input_id in table rather than second query

Removed select before store (made new method store_if_needed if that functionality is required by users)
and added option in AnalysisJobAdaptor::CreateNewJob to pass input_analysis_data_id
so if already know the CreateNewJob will be as fast as before.  Plus there are no limits on the
size of the input_id string.

if one isn't in the database

input_analysis_data_id int(10) which joins to analysis_data table.
added output_analysis_data_id int(10) for storing output_id
External analysis_data.data is LongText which will allow much longer
parameter sets to be passed around than was previously possible.
AnalysisData will also allow processes to manually store 'other' data and
pass it around via ID reference now.

isn't a corresponding Analysis entry in the analysis table

Estentially a mini filesystem so that data that would normally be stored in
NFS files and referenced via a path, can now be stored in the database and
referenced via a dbID. Data is a LONGTEXT.
Can be used to store configuration data, paramater strings,
BLOSSUM matrix data, uuencode of binary data .....

Added get_available_adaptors to get the pairs of name / adaptor modules. This should make it easier to read etc

an analysis if one of it's conditions are not fullfilled.  Needed for case
when system is done, and new data is flowed through the system (progressive runs).

each cycle of loop.  This is to even out the start/stop waves to make it
easier for others to get jobs started on LSF and to reduce
the startup mysql load that can happen when 700 workers all birth at once.
Defaults to 50 (every 5 minutes), but can be altered with -wlimit option

worker request by number of jobs PENDing to prevent excessive queuing of workers.

If not a clean exit, it will record it as a FATALITY and reset it's jobs right away.

should also specify logic_name or analysis_id so that the input_id is run on the
correct analysis.  Doesn't insert job into database. Designed for testing RunnableDB's
but may prove useful in other contexts.

added methods reset_job and global_cleanup to Bio::EnsEMBL::Pipeline::RunnableDB via category extension.
Worker calls global_cleanup on it's runnableDB after all jobs are done.

turn disconnect ON, when there will be lots of them and they have
moments when there will be little DB activity.  The new disconnect system
disconnects so much, that it's slower than before, so must use sparingly.

output jobs) is it needs a fast database, so don't disconnect_when_inactive

created new() methods where needed, replaced throw, rearrange as needed