Commit 5c0e05f0 authored by Brandon Walts's avatar Brandon Walts
Browse files

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 !)
parents 5457428f 02318e02
......@@ -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,
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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;
......
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