Added Parse::RecDescent to the cpanfile#
Moved OverallGroupsetQC to RunnableDB/GeneTrees/
Moved PerGenomeGroupsetQC to RunnableDB/GeneTrees/
"spec_count" is populated when we store a gene tree
The production table protein_tree_qc is not needed any more
Can produce alignment stats for CDS sequences
Merge branch 'release/76' into release/77

* release/76:
  Can produce alignment stats for CDS sequences
Merge branch 'release/77'

* release/77:
  Can produce alignment stats for CDS sequences
fix the doc
Use $self->db_cmd() in pipeline_create_commands()
Should inherit from EnsemblGeneric_conf
Use the eHive runnable to send HTML emails

This effectively makes the two gene-tree pipelines dependent on eHive v2.2
EGComparaGeneric_conf is redundant with ComparaGeneric_conf
Use $self->db_cmd() instead of $self->dbconn_2_mysql()
Scheme patch for v78
New methods to store the number of *matches
Merge branch 'master' into feature/hmm_classification

* master:
  New methods to store the number of *matches
  Scheme patch for v78
  Use $self->db_cmd() instead of $self->dbconn_2_mysql()
  EGComparaGeneric_conf is redundant with ComparaGeneric_conf
  Use the eHive runnable to send HTML emails
  Should inherit from EnsemblGeneric_conf
  Use $self->db_cmd() in pipeline_create_commands()
  fix the doc
  Can produce alignment stats for CDS sequences
  The production table protein_tree_qc is not needed any more
  "spec_count" is populated when we store a gene tree
  Moved PerGenomeGroupsetQC to RunnableDB/GeneTrees/
  Moved OverallGroupsetQC to RunnableDB/GeneTrees/
  Added Parse::RecDescent to the cpanfile#

Conflicts:
	modules/Bio/EnsEMBL/Compara/RunnableDB/DBMergeCheck.pm
Schema update: NULL in paf table
Schema change: new hmm_annot tables