GitLab

modified  Bio::EnsEMBL::Analysis::stats to not do any exception catching
if  AnalysisStatsAdaptor->fetch_by_analysis_id fails there is something
very wrong and the exception should propogate out and cause the program to fail

Bio::EnsEMBL::Analysis::RunnableDB via namespace extension syntax
so that hive system can use analysis.modules that inherit from Bio::EnsEMBL::Analysis::RunnableDB

which takes a hash ref as a parameter and returns a string which can
be evaled back to the hash.  $hash_ref = eval(encode_hash($hash_ref));

so that branch_code is set explicitly rather than replying on the return
value of the write_output method.  Switched Worker.pm to use this value.

if one isn't in the database

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.

analysis objects adaptor to fetch the corresponding stats object.
Important to use correct db connection since the analysis objects may be
network distributed across multiple databases

URL's to specify analysis objects from mysql databases distributed
across a network.  AnalysisJobAdaptor was switched to create jobs with
a cless method that gets the db connection from the analysis object that
is passed.  Thus the system now exists in a distributed state.
The dataflow rule also implements branching via the branch_code.
SimpleRule will be deprecated.

the analysis table/object.  New object class and tables includes a good
guess of what kind of stats I'll need for the Queen to monitor a hive
Also cleaned up some bugs caused by the extraction from compara.