From cf398b08394fc5eccdc59d36391ec7450b62dce9 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 11 Feb 2009 09:34:57 +0000
Subject: [PATCH] *** empty log message ***
---
misc-scripts/id_mapping/default.conf | 2 +-
misc-scripts/surgery/convert120_130.pl | 93 ------
misc-scripts/surgery/convert_6_main.pl | 99 ------
misc-scripts/surgery/convert_7a_main.pl | 99 ------
.../xref_mapping/XrefParser/VbGFF3Parser.pm | 2 +-
misc-scripts/xref_mapping/compare_mapping.pl | 2 +-
.../xref_projection/project_display_xrefs.pl | 2 +-
misc-scripts/xref_projection/release_37.conf | 288 ------------------
misc-scripts/xref_projection/release_38.conf | 288 ------------------
misc-scripts/xref_projection/release_47.ini | 189 ------------
.../xref_projection/submit_projections.pl | 2 +-
11 files changed, 5 insertions(+), 1061 deletions(-)
delete mode 100644 misc-scripts/surgery/convert120_130.pl
delete mode 100644 misc-scripts/surgery/convert_6_main.pl
delete mode 100644 misc-scripts/surgery/convert_7a_main.pl
delete mode 100644 misc-scripts/xref_projection/release_37.conf
delete mode 100644 misc-scripts/xref_projection/release_38.conf
delete mode 100644 misc-scripts/xref_projection/release_47.ini
diff --git a/misc-scripts/id_mapping/default.conf b/misc-scripts/id_mapping/default.conf
index 8d5b95c597..ad5168f1e4 100644
--- a/misc-scripts/id_mapping/default.conf
+++ b/misc-scripts/id_mapping/default.conf
@@ -21,7 +21,7 @@ sourcedbname = pm2_pan_troglodytes_core_40_3c
targethost = ens-research
targetport = 3306
targetuser = ensadmin
-targetpass = ensembl
+targetpass = PASS
targetdbname = pm2_pan_troglodytes_core_41_21
; caching
diff --git a/misc-scripts/surgery/convert120_130.pl b/misc-scripts/surgery/convert120_130.pl
deleted file mode 100644
index 13149d44cb..0000000000
--- a/misc-scripts/surgery/convert120_130.pl
+++ /dev/null
@@ -1,93 +0,0 @@
-# script to convert 120 database to 130 database
-# uses SchemaConvert
-# see doc there
-
-
-use SchemaConverter;
-use DBI;
-
-my $sourcedbh = DBI->connect("dbi:mysql:host=ensrv3.sanger.ac.uk;database=homo_sapiens_core_120", "ensro");
-my $targetdbh = DBI->connect("dbi:mysql:host=ecs1f.sanger.ac.uk;database=arne_ens130", "ensadmin", "ensembl");
-
-my $sc = SchemaConverter->new( $sourcedbh, $targetdbh );
-$sc->tmp_dir( "/work1/stabenau/db" );
-
-
-$sc->custom_select( "assembly", "select s.fpcctg_name, c.chromosome_id, s.raw_id, s.chr_start, s.chr_end, s.fpcctg_start, s.fpcctg_end, s.raw_start, s.raw_end, s.raw_ori, s.type from chromosome c, static_golden_path s where s.chr_name = c.name" );
-
-$sc->table_rename( "analysisprocess", "analysis" );
-$sc->column_rename( "analysis", "analysisId", "analysis_id" );
-
-$sc->column_rename( "contig", "internal_id", "contig_id" );
-$sc->column_rename( "contig", "id", "name" );
-$sc->column_rename( "contig", "clone", "clone_id" );
-$sc->column_rename( "contig", "dna", "dna_id" );
-$sc->column_rename( "contig", "chromosomeId", "chromosome_id" );
-$sc->column_rename( "contig", "international_id", "international_name" );
-
-$sc->column_rename( "clone", "internal_id", "clone_id" );
-$sc->column_rename( "clone", "id", "name" );
-$sc->column_rename( "clone", "embl_id", "embl_acc" );
-
-$sc->custom_select( "map_density", "select c.chromosome_id, m.chr_start, m.chr_end, m.type, m.value from chromosome c, map_density m where m.chr_name = c.name" );
-
-
-$sc->column_rename( "dna", "id", "dna_id" );
-
-$sc->table_skip( "exon_feature" );
-$sc->table_skip( "simple_feature" );
-$sc->table_skip( "dna_align_feature" );
-$sc->table_skip( "protein_align_feature" );
-$sc->table_skip( "repeat_feature" );
-$sc->table_skip( "repeat" );
-$sc->table_skip( "assembly_locations" );
-
-$sc->table_rename( "objectXref", "object_xref" );
-$sc->column_rename( "object_xref", "objectxrefId","object_xref_id" );
-$sc->column_rename( "object_xref", "xrefId", "xref_id" );
-
-$sc->table_rename( "identityXref", "identity_xref" );
-$sc->column_rename( "identity_xref", "objectxrefId","object_xref_id" );
-
-$sc->table_rename( "Xref", "xref" );
-$sc->column_rename( "xref", "xrefId", "xref_id" );
-$sc->column_rename( "xref", "externalDBId", "external_db_id" );
-$sc->column_rename( "xref", "dbprimary_id", "dbprimary_acc" );
-$sc->column_rename( "xref", "display_id", "display_label" );
-
-$sc->table_rename( "externalSynonym", "external_synonym" );
-$sc->column_rename( "external_synonym", "xrefId", "xref_id" );
-
-$sc->table_rename( "externalDB", "external_db" );
-$sc->column_rename( "external_db", "externalDBId", "external_db_id" );
-
-$sc->column_skip( "supporting_feature", "contig_id" );
-
-$sc->column_rename( "protein_feature", "id", "protein_feature_id" );
-$sc->column_rename( "protein_feature", "translation", "translation_id" );
-$sc->column_rename( "protein_feature", "analysis", "analysis_id" );
-$sc->column_rename( "protein_feature", "hstart", "hit_start" );
-$sc->column_rename( "protein_feature", "hend", "hit_end" );
-$sc->column_rename( "protein_feature", "hid", "hit_id" );
-$sc->column_rename( "protein_feature", "perc_id", "perc_ident" );
-
-$sc->column_rename( "exon", "seq_start", "contig_start" );
-$sc->column_rename( "exon", "seq_end", "contig_end" );
-$sc->column_rename( "exon", "strand", "contig_strand" );
-
-$sc->column_rename( "gene", "analysisId", "analysis_id" );
-
-$sc->table_rename( "repeat_feature", "repeat_feature" );
-
-$sc->column_rename( "supporting_feature", "hid", "hit_id" );
-$sc->column_rename( "supporting_feature", "hstart", "hit_start" );
-$sc->column_rename( "supporting_feature", "hend", "hit_end" );
-$sc->column_rename( "supporting_feature", "seq_start", "contig_start" );
-$sc->column_rename( "supporting_feature", "seq_end", "contig_end" );
-$sc->column_rename( "supporting_feature", "hstrand", "hit_strand" );
-$sc->column_rename( "supporting_feature", "analysis", "analysis_id" );
-
-$sc->transfer();
-
-
-
diff --git a/misc-scripts/surgery/convert_6_main.pl b/misc-scripts/surgery/convert_6_main.pl
deleted file mode 100644
index 5aba84568d..0000000000
--- a/misc-scripts/surgery/convert_6_main.pl
+++ /dev/null
@@ -1,99 +0,0 @@
-# script to convert 120 database to 130 database
-# uses SchemaConvert
-# see doc there
-
-
-use SchemaConverter;
-use DBI;
-
-my $sourcedbh = DBI->connect("dbi:mysql:host=ecs2d;database=homo_sapiens_core_6_28", "ensro");
-my $targetdbh = DBI->connect("dbi:mysql:host=ecs1c.sanger.ac.uk;database=arne_main_28", "ensadmin", "ensembl");
-
-my $sc = SchemaConverter->new( $sourcedbh, $targetdbh );
-$sc->tmp_dir( "/acari/work1/stabenau/db" );
-
-
-$sc->custom_select( "assembly", "select s.fpcctg_name, c.chromosome_id, s.raw_id, s.chr_start, s.chr_end, s.fpcctg_start, s.fpcctg_end, s.fpcctg_ori, s.raw_start, s.raw_end, s.raw_ori, s.type from chromosome c, static_golden_path s where s.chr_name = c.name" );
-
-$sc->table_rename( "analysisprocess", "analysis" );
-$sc->column_rename( "analysis", "analysisId", "analysis_id" );
-
-$sc->column_rename( "contig", "internal_id", "contig_id" );
-$sc->column_rename( "contig", "id", "name" );
-$sc->column_rename( "contig", "clone", "clone_id" );
-$sc->column_rename( "contig", "dna", "dna_id" );
-$sc->column_rename( "contig", "chromosomeId", "chromosome_id" );
-$sc->column_rename( "contig", "international_id", "international_name" );
-
-$sc->column_rename( "clone", "internal_id", "clone_id" );
-$sc->column_rename( "clone", "id", "name" );
-$sc->column_rename( "clone", "embl_id", "embl_acc" );
-
-$sc->custom_select( "map_density", "select c.chromosome_id, m.chr_start, m.chr_end, m.type, m.value from chromosome c, map_density m where m.chr_name = c.name" );
-$sc->custom_select( "karyotype", "select c.chromosome_id, k.chr_start, k.chr_end, k.band, k.stain from chromosome c, karyotype k where k.chr_name = c.name" );
-
-
-$sc->column_rename( "dna", "id", "dna_id" );
-$sc->big_table( "dna" );
-
-$sc->table_skip( "exon_feature" );
-$sc->table_skip( "simple_feature" );
-$sc->table_skip( "dna_align_feature" );
-$sc->table_skip( "protein_align_feature" );
-$sc->table_skip( "repeat_feature" );
-$sc->table_skip( "repeat_consensus" );
-$sc->table_skip( "assembly_locations" );
-$sc->table_skip( "landmark_marker" );
-$sc->table_skip( "prediction_transcript" );
-$sc->table_skip( "supporting_feature" );
-
-$sc->table_rename( "objectXref", "object_xref" );
-$sc->column_rename( "object_xref", "objectxrefId","object_xref_id" );
-$sc->column_rename( "object_xref", "xrefId", "xref_id" );
-
-$sc->table_rename( "identityXref", "identity_xref" );
-$sc->column_rename( "identity_xref", "objectxrefId","object_xref_id" );
-
-$sc->table_rename( "Xref", "xref" );
-$sc->column_rename( "xref", "xrefId", "xref_id" );
-$sc->column_rename( "xref", "externalDBId", "external_db_id" );
-$sc->column_rename( "xref", "dbprimary_id", "dbprimary_acc" );
-$sc->column_rename( "xref", "display_id", "display_label" );
-
-$sc->table_rename( "externalSynonym", "external_synonym" );
-$sc->column_rename( "external_synonym", "xrefId", "xref_id" );
-
-$sc->table_rename( "externalDB", "external_db" );
-$sc->column_rename( "external_db", "externalDBId", "external_db_id" );
-
-$sc->column_skip( "supporting_feature", "contig_id" );
-
-$sc->column_rename( "protein_feature", "id", "protein_feature_id" );
-$sc->column_rename( "protein_feature", "translation", "translation_id" );
-$sc->column_rename( "protein_feature", "analysis", "analysis_id" );
-$sc->column_rename( "protein_feature", "hstart", "hit_start" );
-$sc->column_rename( "protein_feature", "hend", "hit_end" );
-$sc->column_rename( "protein_feature", "hid", "hit_id" );
-$sc->column_rename( "protein_feature", "perc_id", "perc_ident" );
-
-$sc->column_rename( "exon", "seq_start", "contig_start" );
-$sc->column_rename( "exon", "seq_end", "contig_end" );
-$sc->column_rename( "exon", "strand", "contig_strand" );
-
-$sc->column_rename( "gene", "analysisId", "analysis_id" );
-$sc->column_skip( "transcript","exon_count" );
-$sc->column_skip( "gene", "transcript_count" );
-
-$sc->column_rename( "supporting_feature", "hid", "hit_id" );
-$sc->column_rename( "supporting_feature", "hstart", "hit_start" );
-$sc->column_rename( "supporting_feature", "hend", "hit_end" );
-$sc->column_rename( "supporting_feature", "seq_start", "contig_start" );
-$sc->column_rename( "supporting_feature", "seq_end", "contig_end" );
-$sc->column_rename( "supporting_feature", "hstrand", "hit_strand" );
-$sc->column_rename( "supporting_feature", "analysis", "analysis_id" );
-
-$sc->clear_target();
-$sc->transfer();
-
-
-
diff --git a/misc-scripts/surgery/convert_7a_main.pl b/misc-scripts/surgery/convert_7a_main.pl
deleted file mode 100644
index e11d070752..0000000000
--- a/misc-scripts/surgery/convert_7a_main.pl
+++ /dev/null
@@ -1,99 +0,0 @@
-# script to convert 120 database to 130 database
-# uses SchemaConvert
-# see doc there
-
-
-use SchemaConverter;
-use DBI;
-
-my $sourcedbh = DBI->connect("dbi:mysql:host=ecs3b;database=homo_sapiens_embl_7_29", "ensro");
-my $targetdbh = DBI->connect("dbi:mysql:host=ecs1c.sanger.ac.uk;database=arne_embl_29", "ensadmin", "ensembl");
-
-my $sc = SchemaConverter->new( $sourcedbh, $targetdbh );
-$sc->tmp_dir( "/acari/work1/stabenau/db" );
-
-
-$sc->custom_select( "assembly", "select s.fpcctg_name, c.chromosome_id, s.raw_id, s.chr_start, s.chr_end, s.fpcctg_start, s.fpcctg_end, s.fpcctg_ori, s.raw_start, s.raw_end, s.raw_ori, s.type from chromosome c, static_golden_path s where s.chr_name = c.name" );
-
-$sc->table_rename( "analysisprocess", "analysis" );
-$sc->column_rename( "analysis", "analysisId", "analysis_id" );
-
-$sc->column_rename( "contig", "internal_id", "contig_id" );
-$sc->column_rename( "contig", "id", "name" );
-$sc->column_rename( "contig", "clone", "clone_id" );
-$sc->column_rename( "contig", "dna", "dna_id" );
-$sc->column_rename( "contig", "chromosomeId", "chromosome_id" );
-$sc->column_rename( "contig", "offset", "embl_offset" );
-
-$sc->column_rename( "clone", "internal_id", "clone_id" );
-$sc->column_rename( "clone", "id", "name" );
-$sc->column_rename( "clone", "embl_id", "embl_acc" );
-
-$sc->custom_select( "map_density", "select c.chromosome_id, m.chr_start, m.chr_end, m.type, m.value from chromosome c, map_density m where m.chr_name = c.name" );
-$sc->custom_select( "karyotype", "select c.chromosome_id, k.chr_start, k.chr_end, k.band, k.stain from chromosome c, karyotype k where k.chr_name = c.name" );
-
-
-$sc->column_rename( "dna", "id", "dna_id" );
-$sc->big_table( "dna" );
-
-$sc->table_skip( "exon_feature" );
-$sc->table_skip( "simple_feature" );
-$sc->table_skip( "dna_align_feature" );
-$sc->table_skip( "protein_align_feature" );
-$sc->table_skip( "repeat_feature" );
-$sc->table_skip( "repeat_consensus" );
-$sc->table_skip( "assembly_locations" );
-$sc->table_skip( "landmark_marker" );
-$sc->table_skip( "prediction_transcript" );
-$sc->table_skip( "supporting_feature" );
-
-$sc->table_rename( "objectXref", "object_xref" );
-$sc->column_rename( "object_xref", "objectxrefId","object_xref_id" );
-$sc->column_rename( "object_xref", "xrefId", "xref_id" );
-
-$sc->table_rename( "identityXref", "identity_xref" );
-$sc->column_rename( "identity_xref", "objectxrefId","object_xref_id" );
-
-$sc->table_rename( "Xref", "xref" );
-$sc->column_rename( "xref", "xrefId", "xref_id" );
-$sc->column_rename( "xref", "externalDBId", "external_db_id" );
-$sc->column_rename( "xref", "dbprimary_id", "dbprimary_acc" );
-$sc->column_rename( "xref", "display_id", "display_label" );
-
-$sc->table_rename( "externalSynonym", "external_synonym" );
-$sc->column_rename( "external_synonym", "xrefId", "xref_id" );
-
-$sc->table_rename( "externalDB", "external_db" );
-$sc->column_rename( "external_db", "externalDBId", "external_db_id" );
-
-$sc->column_skip( "supporting_feature", "contig_id" );
-
-$sc->column_rename( "protein_feature", "id", "protein_feature_id" );
-$sc->column_rename( "protein_feature", "translation", "translation_id" );
-$sc->column_rename( "protein_feature", "analysis", "analysis_id" );
-$sc->column_rename( "protein_feature", "hstart", "hit_start" );
-$sc->column_rename( "protein_feature", "hend", "hit_end" );
-$sc->column_rename( "protein_feature", "hid", "hit_id" );
-$sc->column_rename( "protein_feature", "perc_id", "perc_ident" );
-
-$sc->column_rename( "exon", "seq_start", "contig_start" );
-$sc->column_rename( "exon", "seq_end", "contig_end" );
-$sc->column_rename( "exon", "strand", "contig_strand" );
-
-$sc->column_rename( "gene", "analysisId", "analysis_id" );
-$sc->column_skip( "transcript","exon_count" );
-$sc->column_skip( "gene", "transcript_count" );
-
-$sc->column_rename( "supporting_feature", "hid", "hit_id" );
-$sc->column_rename( "supporting_feature", "hstart", "hit_start" );
-$sc->column_rename( "supporting_feature", "hend", "hit_end" );
-$sc->column_rename( "supporting_feature", "seq_start", "contig_start" );
-$sc->column_rename( "supporting_feature", "seq_end", "contig_end" );
-$sc->column_rename( "supporting_feature", "hstrand", "hit_strand" );
-$sc->column_rename( "supporting_feature", "analysis", "analysis_id" );
-
-$sc->clear_target();
-$sc->transfer();
-
-
-
diff --git a/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm b/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
index 950efaa284..7e516a65d3 100644
--- a/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
@@ -5,7 +5,7 @@ use warnings;
use File::Basename;
use Bio::SeqIO;
-# perl xref_parser.pl -user ensadmin -pass ensembl -host genebuild2 -dbname snr_anopheles_gambiae_48_xref_test -species anopheles_gambiae -source ARRAY_JHSPH_AGGAMBER_15k_v1 -download_path $mywork/VB_xref/downloads/ -checkdownload
+# perl xref_parser.pl -user ensadmin -pass PASS -host genebuild2 -dbname snr_anopheles_gambiae_48_xref_test -species anopheles_gambiae -source ARRAY_JHSPH_AGGAMBER_15k_v1 -download_path $mywork/VB_xref/downloads/ -checkdownload
use base qw( XrefParser::CoordinateParser );
diff --git a/misc-scripts/xref_mapping/compare_mapping.pl b/misc-scripts/xref_mapping/compare_mapping.pl
index b96a310a00..3de82ba096 100644
--- a/misc-scripts/xref_mapping/compare_mapping.pl
+++ b/misc-scripts/xref_mapping/compare_mapping.pl
@@ -9,7 +9,7 @@
# ADDITIONALLY
# read in the synonym conversion. This is created with something like:-
-#mysql -hecs4 -P3350 -uensadmin -pensembl -Dianl_xref_test -e"select x.accession, s.synonym from synonym s, xref x where x.xref_id = s.xref_id" > xref_synonym.txt
+#mysql -hecs4 -P3350 -uensadmin -pPASS -Dianl_xref_test -e"select x.accession, s.synonym from synonym s, xref x where x.xref_id = s.xref_id" > xref_synonym.txt
#ALSO get list of deleted accesions no need to look at these.
#down load wget http://us.expasy.org/txt/delac_tr.txt
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 2898019d65..e054dce441 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -875,7 +875,7 @@ sub usage {
e.g
- perl project_display_xrefs.pl --conf compara_only.ini --host ens-staging -user ensadmin -pass ensembl -version 47 -names -delete_names -from human -to dog -nobackup -no_database
+ perl project_display_xrefs.pl --conf compara_only.ini --host ens-staging -user ensadmin -pass PASS -version 47 -names -delete_names -from human -to dog -nobackup -no_database
EOF
diff --git a/misc-scripts/xref_projection/release_37.conf b/misc-scripts/xref_projection/release_37.conf
deleted file mode 100644
index 72f17884bf..0000000000
--- a/misc-scripts/xref_projection/release_37.conf
+++ /dev/null
@@ -1,288 +0,0 @@
-#
-# Example of configuration file used by Bio::EnsEMBL::Registry::load_all method
-# to store/register all kind of Adaptors.
-
-use strict;
-use Bio::EnsEMBL::Utils::ConfigRegistry;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
-
-my @aliases;
-
-new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-host => 'ia64f',
- -user => 'ensro',
- -port => 3306,
- -species => 'compara37',
- -dbname => 'abel_compara_homology_37');
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Anopheles gambiae',
- -group => 'core',
- -dbname => 'anopheles_gambiae_core_37_3');
-
-@aliases = ('mosquito');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Anopheles gambiae",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Apis mellifera',
- -group => 'core',
- -dbname => 'apis_mellifera_core_37_2d');
-
-@aliases = ('bee');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Apis mellifera",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Bos taurus',
- -group => 'core',
- -dbname => 'bos_taurus_core_37_2a');
-
-@aliases = ('cow');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Bos taurus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Caenorhabditis elegans',
- -group => 'core',
- -dbname => 'caenorhabditis_elegans_core_37_150');
-
-@aliases = ('elegans');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Caenorhabditis elegans",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Canis familiaris',
- -group => 'core',
- -dbname => 'canis_familiaris_core_37_1f');
-
-@aliases = ('dog');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Canis familiaris",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Ciona intestinalis',
- -group => 'core',
- -dbname => 'ciona_intestinalis_core_37_2');
-
-@aliases = ('ciona');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Ciona intestinalis",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Danio rerio',
- -group => 'core',
- -dbname => 'danio_rerio_core_37_5d');
-
-@aliases = ('zebrafish');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Danio rerio",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Drosophila melanogaster',
- -group => 'core',
- -dbname => 'drosophila_melanogaster_core_37_4e');
-
-@aliases = ('fly');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Drosophila melanogaster",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Fugu rubripes',
- -group => 'core',
- -dbname => 'fugu_rubripes_core_37_4a');
-
-@aliases = ('fugu');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Fugu rubripes",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Gallus gallus',
- -group => 'core',
- -dbname => 'gallus_gallus_core_37_1m');
-
-@aliases = ('chicken');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Gallus gallus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Homo sapiens',
- -group => 'core',
- -dbname => 'homo_sapiens_core_37_35j');
-
-@aliases = ('human');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Homo sapiens",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Rhesus macaque',
- -group => 'core',
- -dbname => 'macaca_mulatta_core_37_1a');
-
-@aliases = ('macaque');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rhesus macaque",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Monodelphis domestica',
- -group => 'core',
- -dbname => 'monodelphis_domestica_core_37_2a');
-
-@aliases = ('opossum');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Monodelphis domestica",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Mus musculus',
- -group => 'core',
- -dbname => 'mus_musculus_core_37_34e');
-
-@aliases = ('mouse');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Mus musculus",
- -alias => \@aliases);
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Pan troglodytes',
- -group => 'core',
- -dbname => 'pan_troglodytes_core_37_3a');
-
-@aliases = ('chimp');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Pan troglodytes",
- -alias => \@aliases);
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Rattus norvegicus',
- -group => 'core',
- -dbname => 'rattus_norvegicus_core_37_34g');
-
-@aliases = ('rat');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rattus norvegicus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Saccharomyces_cerevisiae',
- -group => 'core',
- -dbname => 'saccharomyces_cerevisiae_core_37_1d');
-
-@aliases = ('yeast');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Saccharomyces_cerevisiae",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Tetraodon nigroviridis',
- -group => 'core',
- -dbname => 'tetraodon_nigroviridis_core_37_1e');
-
-@aliases = ('tetraodon');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Tetraodon nigroviridis",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Xenopus tropicalis',
- -group => 'core',
- -dbname => 'xenopus_tropicalis_core_37_4');
-
-@aliases = ('xenopus');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Xenopus tropicalis",
- -alias => \@aliases);
-
-
-
-1;
diff --git a/misc-scripts/xref_projection/release_38.conf b/misc-scripts/xref_projection/release_38.conf
deleted file mode 100644
index e3adffea1b..0000000000
--- a/misc-scripts/xref_projection/release_38.conf
+++ /dev/null
@@ -1,288 +0,0 @@
-#
-# Example of configuration file used by Bio::EnsEMBL::Registry::load_all method
-# to store/register all kind of Adaptors.
-
-use strict;
-use Bio::EnsEMBL::Utils::ConfigRegistry;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
-
-my @aliases;
-
-new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-host => 'ia64f',
- -user => 'ensro',
- -port => 3306,
- -species => 'compara37',
- -dbname => 'abel_compara_homology_37');
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Anopheles gambiae',
- -group => 'core',
- -dbname => 'anopheles_gambiae_core_38_3a');
-
-@aliases = ('mosquito');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Anopheles gambiae",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Apis mellifera',
- -group => 'core',
- -dbname => 'apis_mellifera_core_38_2d');
-
-@aliases = ('bee');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Apis mellifera",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Bos taurus',
- -group => 'core',
- -dbname => 'bos_taurus_core_38_2b');
-
-@aliases = ('cow');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Bos taurus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Caenorhabditis elegans',
- -group => 'core',
- -dbname => 'caenorhabditis_elegans_core_38_150a');
-
-@aliases = ('elegans');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Caenorhabditis elegans",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Canis familiaris',
- -group => 'core',
- -dbname => 'canis_familiaris_core_38_1g');
-
-@aliases = ('dog');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Canis familiaris",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Ciona intestinalis',
- -group => 'core',
- -dbname => 'ciona_intestinalis_core_38_2a');
-
-@aliases = ('ciona');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Ciona intestinalis",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Danio rerio',
- -group => 'core',
- -dbname => 'danio_rerio_core_38_5e');
-
-@aliases = ('zebrafish');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Danio rerio",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Drosophila melanogaster',
- -group => 'core',
- -dbname => 'drosophila_melanogaster_core_38_4e');
-
-@aliases = ('fly');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Drosophila melanogaster",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Fugu rubripes',
- -group => 'core',
- -dbname => 'fugu_rubripes_core_38_4a');
-
-@aliases = ('fugu');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Fugu rubripes",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Gallus gallus',
- -group => 'core',
- -dbname => 'gallus_gallus_core_38_1n');
-
-@aliases = ('chicken');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Gallus gallus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Homo sapiens',
- -group => 'core',
- -dbname => 'homo_sapiens_core_38_36');
-
-@aliases = ('human');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Homo sapiens",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Rhesus macaque',
- -group => 'core',
- -dbname => 'macaca_mulatta_core_38_1b');
-
-@aliases = ('macaque');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rhesus macaque",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Monodelphis domestica',
- -group => 'core',
- -dbname => 'monodelphis_domestica_core_38_2b');
-
-@aliases = ('opossum');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Monodelphis domestica",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Mus musculus',
- -group => 'core',
- -dbname => 'mus_musculus_core_38_35');
-
-@aliases = ('mouse');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Mus musculus",
- -alias => \@aliases);
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Pan troglodytes',
- -group => 'core',
- -dbname => 'pan_troglodytes_core_38_3b');
-
-@aliases = ('chimp');
-
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Pan troglodytes",
- -alias => \@aliases);
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Rattus norvegicus',
- -group => 'core',
- -dbname => 'rattus_norvegicus_core_38_34h');
-
-@aliases = ('rat');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rattus norvegicus",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Saccharomyces_cerevisiae',
- -group => 'core',
- -dbname => 'saccharomyces_cerevisiae_core_38_1d');
-
-@aliases = ('yeast');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Saccharomyces_cerevisiae",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Tetraodon nigroviridis',
- -group => 'core',
- -dbname => 'tetraodon_nigroviridis_core_38_1e');
-
-@aliases = ('tetraodon');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Tetraodon nigroviridis",
- -alias => \@aliases);
-
-
-new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => 'ecs2',
- -user => 'ensadmin',
- -pass => 'ensembl',
- -port => 3364,
- -species => 'Xenopus tropicalis',
- -group => 'core',
- -dbname => 'xenopus_tropicalis_core_38_41');
-
-@aliases = ('xenopus');
-
-Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Xenopus tropicalis",
- -alias => \@aliases);
-
-
-
-1;
diff --git a/misc-scripts/xref_projection/release_47.ini b/misc-scripts/xref_projection/release_47.ini
deleted file mode 100644
index 75f43bf355..0000000000
--- a/misc-scripts/xref_projection/release_47.ini
+++ /dev/null
@@ -1,189 +0,0 @@
-; Configuration file for release 47
-
-[default]
-user = ensadmin
-pass = ensembl
-host = ens-staging
-group = Core
-
-[Compara]
-group = Compara
-dbname = ensembl_compara_47
-
-[Aedes]
-species = Aedes aeqypti
-alias = aedes
-dbname = aedes_aegypti_core_47_1a
-
-[Anopheles]
-species = Anopheles gambiae
-alias = anopheles
-alias = mosquito
-dbname = anopheles_gambiae_core_47_3i
-
-[Cow]
-species = Bos taurus
-alias = cow
-dbname = bos_taurus_core_47_3d
-
-[Elegans]
-species = Caenorhabditis elegans
-alias = elegans
-dbname = caenorhabditis_elegans_core_47_180
-
-[Dog]
-species = Canis familiaris
-alias = dog
-dbname = canis_familiaris_core_47_2e
-
-[Guinea Pig]
-species = Cavia porcellus
-alias = guinea_pig
-dbname = cavia_porcellus_core_47_1b
-
-[Ciona intestinalis]
-species = Ciona intestinalis
-alias = intestinalis
-dbname = ciona_intestinalis_core_47_2g
-
-[Ciona Savignyi]
-species = Ciona savignyi
-alias = savignyi
-dbname = ciona_savignyi_core_47_2e
-
-[Zebrafish]
-species = Danio rerio
-alias = danio
-alias = zebrafish
-dbname = danio_rerio_core_47_7a
-
-[Armadillo]
-species = Dasypus novemcinctus
-alias = armadillo
-dbname = dasypus_novemcinctus_core_47_1d
-
-[Drosophila]
-species = Drosophila melanogaster
-alias = drosophila
-dbname = drosophila_melanogaster_core_47_43b
-
-[Small hedgehog]
-species = Echinops telfairi
-alias = small_hedgehog
-dbname = echinops_telfairi_core_47_1d
-
-[Euroipean hedgehog]
-species = Erinaceus europaeus
-alias = european_hedgehog
-dbname = erinaceus_europaeus_core_47_1b
-
-[Cat]
-species = Felis catus
-alias = cat
-dbname = felis_catus_core_47_1b
-
-[Chicken]
-species = Gallus gallus
-alias = chicken
-dbname = gallus_gallus_core_47_2e
-
-[Stickleback]
-species = Gasterosteus aculeatus
-alias = stickleback
-dbname = gasterosteus_aculeatus_core_47_1d
-
-[Human]
-species = Homo sapiens
-alias = human
-dbname = homo_sapiens_core_47_36i
-
-[Elephant]
-species = Loxodonta africana
-alias = elephant
-dbname = loxodonta_africana_core_47_1c
-
-[Macaque]
-species = Macaca mulatta
-alias = macaque
-dbname = macaca_mulatta_core_47_10f
-
-[Monodelphis]
-species = Monodelphis domestica
-alias = monodelphis
-alias = opossum
-dbname = monodelphis_domestica_core_47_5b
-
-[Mouse]
-species = Mus musculus
-alias = mouse
-dbname = mus_musculus_core_47_37
-
-[Bat]
-species = Myotis licifugus
-alias = bat
-dbname = myotis_lucifugus_core_47_1c
-
-[Platypus]
-species = Ornithorhynchus anatinus
-alias = platypus
-dbname = ornithorhynchus_anatinus_core_47_1d
-
-[Rabbit]
-species = Oryctolagus cuniculus
-alias = rabbit
-dbname = oryctolagus_cuniculus_core_47_1d
-
-[Medaka]
-species = Oryzias latipes
-alias = medaka
-dbname = oryzias_latipes_core_47_1c
-
-[Galago]
-species = Otolemur garnettii
-alias = galago
-dbname = otolemur_garnettii_core_47_1a
-
-[Chimp]
-species = Pan troglodytes
-alias = chimp
-dbname = pan_troglodytes_core_47_21f
-
-[Rat]
-species = Rattus norvegicus
-alias = rat
-dbname = rattus_norvegicus_core_47_34q
-
-[Yeast]
-species = Saccharomyces cerevisiae
-alias = yeast
-dbname = saccharomyces_cerevisiae_core_47_1g
-
-[European shrew]
-species = Sorex araneus
-alias = european_shrew
-dbname = sorex_araneus_core_47_1a
-
-[Squirrel]
-species = Spermophilus tridecemlineatus
-alias = squirrel
-dbname = spermophilus_tridecemlineatus_core_47_1c
-
-[Fugu]
-species = Takifugu rubripes
-alias = fugu
-dbname = takifugu_rubripes_core_47_4g
-
-[Tetraodon]
-species = Tetraodon nigroviridis
-alias = tetraodon
-dbname = tetraodon_nigroviridis_core_47_1i
-
-[Ground shrew]
-species = Tupaia belangeri
-alias = ground_shrew
-dbname = tupaia_belangeri_core_47_1b
-
-[Xenopus]
-species = Xenopus tropicalis
-alias = xenopus
-dbname = xenopus_tropicalis_core_47_41g
\ No newline at end of file
diff --git a/misc-scripts/xref_projection/submit_projections.pl b/misc-scripts/xref_projection/submit_projections.pl
index 1adad2ab6e..ad27b1745a 100644
--- a/misc-scripts/xref_projection/submit_projections.pl
+++ b/misc-scripts/xref_projection/submit_projections.pl
@@ -14,7 +14,7 @@ my $conf = "release_53.ini"; # registry config file, specifies Compara location
my $host = "ens-staging";
my $port = 3306;
my $user = "ensadmin";
-my $pass = "ensembl";
+my $pass = "PASS";
# load limit for ens-staging MySQL instance above which jobs won't be started
my $limit = 200;
--
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