making Registry code optional (require instead of use everywhere)

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

@@ -61,7 +61,6 @@ use strict;
 use warnings;
 
 use Bio::EnsEMBL::ApiVersion ();
-use Bio::EnsEMBL::Registry;
 
 use Bio::EnsEMBL::Hive::Utils::URL;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
@@ -450,7 +449,6 @@ sub run {
         }
     }
 
-    Bio::EnsEMBL::Registry->no_version_check(1);
     my $hive_dba                     = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url, -no_sql_schema_version_check => 1 );
     my $resource_class_adaptor       = $hive_dba->get_ResourceClassAdaptor;
 

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -99,7 +99,6 @@ package Bio::EnsEMBL::Hive::Process;
 use strict;
 use warnings;
 
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Utils::Exception ('throw');
 
 use Bio::EnsEMBL::Hive::DBSQL::DBConnection;

modules/Bio/EnsEMBL/Hive/Utils.pm

@@ -313,6 +313,7 @@ sub go_figure_dbc {
             my $dba;
             eval {
                 $schema_type ||= 'hive';
+                require Bio::EnsEMBL::Registry;
                 $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($foo, $schema_type);
             };
             if(UNIVERSAL::can($dba, 'dbc')) {

scripts/beekeeper.pl

@@ -25,7 +25,6 @@ main();
 
 sub main {
     $| = 1;
-    Bio::EnsEMBL::Registry->no_version_check(1);
 
         # ok this is a hack, but I'm going to pretend I've got an object here
         # by creating a hash ref and passing it around like an object

scripts/db_cmd.pl

@@ -12,7 +12,6 @@ BEGIN {
 }
 
 use Getopt::Long;
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::Utils::URL;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');
 
@@ -43,6 +42,8 @@ sub main {
 
     } elsif($reg_alias) {
         script_usage(1) if $url;
+
+        require Bio::EnsEMBL::Registry;
         Bio::EnsEMBL::Registry->load_all($reg_conf);
 
         my $species = Bio::EnsEMBL::Registry->get_alias($reg_alias)

scripts/hoover_pipeline.pl

@@ -13,7 +13,6 @@ BEGIN {
 
 
 use Getopt::Long;
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');

scripts/runWorker.pl

@@ -14,13 +14,10 @@ BEGIN {
 
 use Getopt::Long;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::Queen;
 use Bio::EnsEMBL::Hive::Valley;
 
-Bio::EnsEMBL::Registry->no_version_check(1);
-
 my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc);                   # Connection parameters
 my ($resource_class_id, $resource_class_name, $analysis_id, $logic_name, $job_id, $force);  # Task specification parameters
 my ($job_limit, $life_span, $no_cleanup, $no_write, $hive_log_dir, $worker_log_dir, $retry_throwing_jobs, $can_respecialize);   # Worker control parameters
@@ -60,10 +57,6 @@ GetOptions(
 
 if ($help) { script_usage(0); }
 
-if($reg_conf) {     # if reg_conf is defined, we load it regardless of whether it is used to connect to the Hive database or not:
-    Bio::EnsEMBL::Registry->load_all($reg_conf);
-}
-
 my $hive_dba;
 
 if($url or $reg_alias) {

scripts/standaloneJob.pl

@@ -13,7 +13,6 @@ BEGIN {
 
 
 use Getopt::Long qw(:config pass_through);
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::Process;
 use Bio::EnsEMBL::Hive::AnalysisJob;
 use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module', 'parse_cmdline_options', 'stringify', 'destringify');
@@ -39,6 +38,7 @@ if ($help or !$module_or_file) {
 my $runnable_module = load_file_or_module( $module_or_file );
 
 if($reg_conf) {
+    require Bio::EnsEMBL::Registry;
     Bio::EnsEMBL::Registry->load_all($reg_conf);
 }