diff --git a/misc-scripts/alt_alleles/alt_alleles.pl b/misc-scripts/alt_alleles/alt_alleles.pl index 6c234ede9f7de4ef0142a884c9a63bb20cdc3963..2edd6a7d7e28e86957dd63a02e6c439e1fa45085 100644 --- a/misc-scripts/alt_alleles/alt_alleles.pl +++ b/misc-scripts/alt_alleles/alt_alleles.pl @@ -62,7 +62,7 @@ if(!defined($cdbname)){ # my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( - -host => $chost||'ens-staging3', + -host => $chost||'ens-staging1', -user => $cuser||'ensadmin', -pass => $cpass, -group => 'core', @@ -71,7 +71,7 @@ my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( ); my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( - -host => $vhost||'ens-staging3', + -host => $vhost||'ens-staging1', -user => $vuser||'ensadmin', -pass => $vpass, -group => 'vega', diff --git a/misc-scripts/assembly/exon_conservation_check.pl b/misc-scripts/assembly/exon_conservation_check.pl index d399cf44dd408af2ebaca69a529c9816b0bea2f0..d35cb74bcdc1053bd561c55865d9a30ec4ca4c89 100644 --- a/misc-scripts/assembly/exon_conservation_check.pl +++ b/misc-scripts/assembly/exon_conservation_check.pl @@ -77,7 +77,7 @@ if ($support->param('prod_port')) { $prod_port = $support->param('prod_port'); # use Bio::EnsEMBL::Production::DBSQL::DBAdaptor; my $prod_dba = Bio::EnsEMBL::Production::DBSQL::DBAdaptor->new( - -host => 'ens-staging3', + -host => 'ens-staging1', -user => 'ensro', -port => 3306, -dbname => 'ensembl_production', diff --git a/misc-scripts/db/multidb_sql.pl b/misc-scripts/db/multidb_sql.pl index 78dc041c427a42bc74d4badaeec4590dd821f123..77a9b4ee898cbb64ddde4aae84d913b993e83b9a 100644 --- a/misc-scripts/db/multidb_sql.pl +++ b/misc-scripts/db/multidb_sql.pl @@ -36,7 +36,7 @@ my ( @hosts, $host, $user, $pass, $port, $expression, $dbpattern, $file, $result $user = 'ensro' ; $pass = '' ; $port = 3306 ; -@hosts = qw ( ens-staging3 ) ; +@hosts = qw ( ens-staging1 ens-staging2) ; GetOptions( "host|dbhost=s", \$host, "hosts|dbhosts=s", \@hosts, diff --git a/misc-scripts/id_mapping/default.conf b/misc-scripts/id_mapping/default.conf index f090ad20be0e5ca9de2b493768248a25e2c01c33..08df85c524ff2a70b9059e838aa45b0f06ffc2d0 100644 --- a/misc-scripts/id_mapping/default.conf +++ b/misc-scripts/id_mapping/default.conf @@ -36,7 +36,7 @@ targetdbname = sf7_patch_pa_62 ;targetdbname_dna = homo_sapiens_core_62_37g ;; the production database -productionhost = ens-staging3 +productionhost = ens-staging1 productionport = 3306 productionuser = READONLY_USER productiondbname = ensembl_production diff --git a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm index cd716e2ff6e0c1a3ee4fa5b273c3016176f1d572..beb34a238d105cb5074a16ad45719b5066d93ddb 100644 --- a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm @@ -103,8 +103,12 @@ sub run_script { print "Loading the Registry\n" if $verbose; $registry->load_registry_from_multiple_dbs( { - '-host' => 'ens-staging3', + '-host' => 'ens-staging1', '-user' => 'ensro', + }, + { + '-host' => 'ens-staging2', + '-user' => 'ensro', } ); $gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene'); diff --git a/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm b/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm index 093f304f3bb52791a08d257185ae81fe9f84b37b..5ef2408d658af42b1c2a00ea5029146c460d78e6 100644 --- a/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm @@ -71,9 +71,13 @@ sub run_script { if ($project eq 'ensembl') { $registry->load_registry_from_multiple_dbs( { - '-host' => 'ens-staging3', + '-host' => 'ens-staging1', '-user' => 'ensro', }, + { + '-host' => 'ens-staging2', + '-user' => 'ensro', + }, ); } elsif ($project eq 'ensemblgenomes') { diff --git a/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm index 5bee2db4218412638c1cc935f3bd473f6165709b..1d4e77ccd6a36ceeca625fc6c5488f73ec8a0819 100755 --- a/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm @@ -50,7 +50,11 @@ sub run_script { if ($project eq 'ensembl') { $registry->load_registry_from_multiple_dbs( { - '-host' => 'ens-staging3', + '-host' => 'ens-staging1', + '-user' => 'ensro', + }, + { + '-host' => 'ens-staging2', '-user' => 'ensro', }, ); diff --git a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm index 79d918c8687ff52717f1995430d8a82cc22d17ee..7b036fdb1391f351f8637a53eeb6478afb240110 100644 --- a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm @@ -88,9 +88,13 @@ sub run_script { } else { $registry->load_registry_from_multiple_dbs( { - '-host' => 'ens-staging3', + '-host' => 'ens-staging1', '-user' => 'ensro', }, + { + '-host' => 'ens-staging2', + '-user' => 'ensro', + }, ); $dba = $registry->get_DBAdaptor($species_name, 'core'); } diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm index 30128de8ae1ff42e76fb509eaa45071d93e1b50f..a876411f72abee1a463b7207fd45675e1db6423b 100644 --- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm @@ -138,9 +138,13 @@ sub run_script { # Else, database should be on staging $registry->load_registry_from_multiple_dbs( { - -host => 'ens-staging3', + -host => 'ens-staging1', -user => 'ensro', }, + { + -host => 'ens-staging2', + -user => 'ensro', + }, ); $core_dba = $registry->get_DBAdaptor($species_name,'core'); } @@ -159,9 +163,13 @@ sub run_script { # Else database should be on staging $registry->load_registry_from_multiple_dbs( { - -host => 'ens-staging3', + -host => 'ens-staging1', -user => 'ensro', }, + { + -host => 'ens-staging2', + -user => 'ensro', + }, ); $otherf_dba = $registry->get_DBAdaptor($species_name, 'otherfeatures') if !defined($ofhost); if (defined $otherf_dba) { $otherf_dba->dnadb($core_dba); } diff --git a/misc-scripts/xref_mapping/core_vega_link_check.pl b/misc-scripts/xref_mapping/core_vega_link_check.pl index d702d7d9112554e26e676323277dd4853b19c51f..5e59af4cf6b8af93f80167c3a00ed186bf240926 100644 --- a/misc-scripts/xref_mapping/core_vega_link_check.pl +++ b/misc-scripts/xref_mapping/core_vega_link_check.pl @@ -26,12 +26,12 @@ my $species = shift; if($species eq "mouse"){ $reg->load_registry_from_db( - -host => 'ens-staging3', + -host => 'ens-staging2', -user => 'ensro'); } else{ $reg->load_registry_from_db( - -host => 'ens-staging3', + -host => 'ens-staging1', -user => "ensro"); } diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 5e6da7bf5746948929130d26d5a6b3e3567fc250..c28ea6b94abe4b9850dd2afc6ecf5b7a96a566d2 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -1148,7 +1148,7 @@ priority = 3 prio_descr = vega parser = VegaOfficialNameParser release_uri = -data_uri = script:source=>HGNC,host=>ens-staging3, +data_uri = script:source=>HGNC,host=>ens-staging1, #data_uri = script:source=>HGNC,chost=>ens-production,cdbname=>mr6_human_core,vdbhost=>ens-production,vdbname=>mr6_human_vega, @@ -1418,7 +1418,7 @@ priority = 2 prio_descr = vega parser = VegaOfficialNameParser release_uri = -data_uri = script:source=>MGI,host=>ens-staging3, +data_uri = script:source=>MGI,host=>ens-staging2, #data_uri = script:source=>MGI,chost=>ens-production,cdbname=>mr6_mouse_core,vhost=>ens-production,vdbname=>mr6_mouse_vega, [source MGI::mus_musculus#05] @@ -1557,7 +1557,7 @@ priority = 3 prio_descr = vega parser = VegaOfficialNameParser release_uri = -data_uri = script:source=>RGD,host=>ens-staging3, +data_uri = script:source=>RGD,host=>ens-staging2, #data_uri = script:source=>RGD,chost=>genebuild3,cdbname=>db8_rattus_norvegicus_core_77_5,vhost=>genebuild6,vdbname=>db8_rat_vega_77, [source RGD_trans_name] @@ -1577,7 +1577,7 @@ priority = 1 prio_descr = parser = curated_transcriptParser release_uri = -data_uri = script:source=>RGD,host=>ens-staging3, +data_uri = script:source=>RGD,host=>ens-staging2, #data_uri = script:source=>RGD,chost=>ens-staging2,cdbname=>rattus_norvegicus_core_77_5,vdbname=>db8_rat_vega_77,vhost=>genebuild6, [source RefSeq_dna::MULTI-fungi] @@ -3940,7 +3940,7 @@ priority = 1 prio_descr = curated with transcript number postfix parser = curated_transcriptParser release_uri = -data_uri = script:source=>HGNC,host=>ens-staging3, +data_uri = script:source=>HGNC,host=>ens-staging1, #data_uri = script:source=>HGNC,chost=>ens-production,cdbname=>mr6_human_core,vdbname=>mr6_human_vega,vhost=>ens-production, [source PIGGY_curated_transcript::sus_scrofa] @@ -3951,7 +3951,7 @@ priority = 1 prio_descr = curated with transcript number postfix parser = curated_transcriptParser release_uri = -data_uri = script:source=>PIGGY,host=>ens-staging3, +data_uri = script:source=>PIGGY,host=>ens-staging2, #data_uri = script:source=>PIGGY,chost=>ens-production,cdbname=>mr6_pig_core,vdbname=>mr6_pig_vega,vhost=>ens-production, [source PIGGY::sus_scrofa] @@ -3963,7 +3963,7 @@ priority = 1 prio_descr = vega parser = VegaOfficialNameParser release_uri = -data_uri = script:host=>ens-staging3,source=>PIGGY, +data_uri = script:host=>ens-staging2,source=>PIGGY, [source PIGGY_trans_name] name = PIGGY_trans_name @@ -4018,7 +4018,7 @@ priority = 1 prio_descr = parser = curated_transcriptParser release_uri = -data_uri = script:source=>MGI,host=>ens-staging3, +data_uri = script:source=>MGI,host=>ens-staging2, #data_uri = script:source=>MGI,chost=>ens-production,cdbname=>mr6_mouse_core,vdbname=>mr6_pig_vega,vhost=>ens-production, @@ -4126,7 +4126,7 @@ priority = 2 prio_descr = vega parser = VegaOfficialNameParser release_uri = -data_uri = script:source=>ZFIN_ID,host=>ens-staging3, +data_uri = script:source=>ZFIN_ID,host=>ens-staging1, #data_uri = script:source=>ZFIN_ID,chost=>ens-production,cdbname=>mr6_danio_core,vhost=>ens-production,vdbname=>mr6_danio_vega, [source ZFIN_ID::danio_rerio#03] @@ -4149,7 +4149,7 @@ priority = 1 prio_descr = curated with transcript number postfix parser = curated_transcriptParser release_uri = -data_uri = script:source=>ZFIN_ID,host=>ens-staging3, +data_uri = script:source=>ZFIN_ID,host=>ens-staging1, #data_uri = script:source=>ZFIN_ID,chost=>ens-production,cdbname=>mr6_danio_core,vdbname=>mr6_pig_vega,vhost=>ens-production, [source ZFIN_ID_trans_name]