From d3cca3cb0a9d26db51d36fe0f2ea506cad6aca94 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 7 Feb 2014 10:20:27 +0000
Subject: [PATCH] more tweaks: pipeline_name contains rel_with_suffix,
EHIVE_USER/EHIVE_PASS are still checked first, schema_version not duplicated
---
.../Hive/PipeConfig/EnsemblGeneric_conf.pm | 22 ++++++-------------
1 file changed, 7 insertions(+), 15 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm
index b2cdd42d2..da6484936 100644
--- a/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm
@@ -61,23 +61,15 @@ sub default_options {
# [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_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
'rel_with_suffix' => $self->o('ensembl_release').$self->o('rel_suffix'),
- 'user' => 'ensadmin',
- 'password' => $ENV{'ENSADMIN_PSW'} // $self->o('password'), # people will have to make an effort NOT to insert it into config files like .bashrc etc
- 'dbowner' => $ENV{'USER'} // $self->o('dbowner'), # although it is very unlikely $ENV{USER} is not set
- 'pipeline_name' => $self->pipeline_name(),
-
- 'pipeline_db' => {
- -driver => $self->o('hive_driver'),
- -host => $self->o('host'),
- -port => $self->o('port'),
- -user => $self->o('user'),
- -pass => $self->o('password'),
- -dbname => $self->o('dbowner').'_'.$self->o('pipeline_name').'_'.$self->o('rel_with_suffix'), # example of a linked definition (resolved via saturation)
- },
+ 'pipeline_name' => $self->pipeline_name().'_'.$self->o('rel_with_suffix'),
+
+ 'user' => $ENV{'EHIVE_USER'} || 'ensadmin',
+ 'password' => $ENV{'EHIVE_PASS'} // $ENV{'ENSADMIN_PSW'} // $self->o('password'), # people will have to make an effort NOT to insert it into config files like .bashrc etc
};
}
@@ -93,9 +85,9 @@ sub default_options {
sub pipeline_wide_parameters {
my ($self) = @_;
return {
- %{ $self->SUPER::pipeline_wide_parameters() }, # inherit from parent
+ %{ $self->SUPER::pipeline_wide_parameters() }, # inherit from parent
- 'schema_version' => $self->o('ensembl_release'), # keep compatibility with core API
+# 'schema_version' => $self->o('ensembl_release'), # commented out to avoid duplicating 'schema_version' inserted by the schema mysql file
};
}
--
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