Merge branch 'version/2.5'

* version/2.5:
  Fix ensembl_csv_root_dir value setting priorities
  EnsemblGeneric_conf checks for ENSEMBL_ROOT_DIR and ENSEMBL_CSV_ROOT_DIR
  typo
  Don't put the schema definition there, as it may go out of sync (it already has !)

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -6,16 +6,7 @@
 
 =head1 DESCRIPTION
 
-    A data container object (methods are intelligent getters/setters) that corresponds to a row stored in 'dataflow_rule' table:
-
-    CREATE TABLE dataflow_rule (
-        dataflow_rule_id    int(10) unsigned NOT NULL AUTO_INCREMENT,
-        from_analysis_id    int(10) unsigned NOT NULL,
-        branch_code         int(10) default 1 NOT NULL,
-
-        PRIMARY KEY (dataflow_rule_id),
-        UNIQUE (from_analysis_id, to_analysis_url)
-    );
+    A data container object (methods are intelligent getters/setters) that corresponds to a row stored in 'dataflow_rule' table
 
     A dataflow rule is activated when a Bio::EnsEMBL::Hive::AnalysisJob::dataflow_output_id is called at any moment during a RunnableDB's execution.
     The current RunnableDB's analysis ($from_analysis) and the requested $branch_code (1 by default) define the entry conditions,

modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm

@@ -61,7 +61,7 @@ sub default_options {
             #   [bash]      export -n ENSEMBL_CVS_ROOT_DIR  # will stop exporting, but the value in current shell stays as it was
             #   [tcsh]      unsetenv ENSEMBL_CVS_ROOT_DIR   # will destroy the variable even in current shell, and stop exporting
 
-        'ensembl_cvs_root_dir'  => $ENV{'ENSEMBL_CVS_ROOT_DIR'} || $self->o('ensembl_cvs_root_dir'),    # it will make sense to set this variable if you are going to use ehive with ensembl
+	'ensembl_cvs_root_dir'  => $self->o('ensembl_root_dir') || $self->o('ensembl_cvs_root_dir') || $ENV{'ENSEMBL_ROOT_DIR'} || $ENV{'ENSEMBL_CVS_ROOT_DIR'},    # it will make sense to set this variable if you are going to use ehive with ensembl
 
         'ensembl_release'       => Bio::EnsEMBL::ApiVersion::software_version(),                        # snapshot of EnsEMBL Core API version. Please do not change if not sure.
         'rel_suffix'            => '',                                                                  # an empty string by default, a letter otherwise

modules/Bio/EnsEMBL/Hive/ResourceClass.pm

@@ -6,14 +6,7 @@
 
 =head1 DESCRIPTION
 
-    A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_class' table:
-
-    CREATE TABLE resource_class (
-        resource_class_id   int(10) unsigned NOT NULL AUTO_INCREMENT,     # unique internal id
-        name                varchar(40) NOT NULL,
-
-        PRIMARY KEY(resource_class_id)
-    );
+    A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_class' table
 
 =head1 LICENSE
 

modules/Bio/EnsEMBL/Hive/ResourceDescription.pm

@@ -6,16 +6,7 @@
 
 =head1 DESCRIPTION
 
-    A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_description' table:
-
-    CREATE TABLE resource_description (
-        resource_class_id     int(10) unsigned NOT NULL,
-        meadow_type           varchar(40) NOT NULL,
-        submission_cmd_args     VARCHAR(255) NOT NULL DEFAULT '',
-        worker_cmd_args         VARCHAR(255) NOT NULL DEFAULT '',
-
-        PRIMARY KEY(resource_class_id, meadow_type)
-    ) ENGINE=InnoDB;
+    A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_description' table
 
 =head1 LICENSE
 

sql/procedures.mysql

@@ -32,7 +32,7 @@ CONTACT
 --
 -- Usage:
 --       select * from progress;                                         # the whole table (may take ages to generate, depending on the size of your pipeline)
---       select * from progress where logic_name like 'family_blast%';   # only show family_blast-related analyses
+--       select * from progress where analysis_name_and_id like 'family_blast%';   # only show family_blast-related analyses
 --       select * from progress where retry_count>1;                     # only show jobs that have been tried more than once
 
 CREATE OR REPLACE VIEW progress AS

sql/procedures.pgsql

@@ -32,7 +32,7 @@ CONTACT
 --
 -- Usage:
 --       select * from progress;                                         # the whole table (may take ages to generate, depending on the size of your pipeline)
---       select * from progress where logic_name like 'family_blast%';   # only show family_blast-related analyses
+--       select * from progress where analysis_name_and_id like 'family_blast%';   # only show family_blast-related analyses
 --       select * from progress where retry_count>1;                     # only show jobs that have been tried more than once
 
 CREATE OR REPLACE VIEW progress AS

sql/procedures.sqlite

@@ -32,7 +32,7 @@ CONTACT
 --
 -- Usage:
 --       select * from progress;                                         # the whole table (may take ages to generate, depending on the size of your pipeline)
---       select * from progress where logic_name like 'family_blast%';   # only show family_blast-related analyses
+--       select * from progress where analysis_name_and_id like 'family_blast%';   # only show family_blast-related analyses
 --       select * from progress where retry_count>1;                     # only show jobs that have been tried more than once
 
 DROP VIEW IF EXISTS progress;