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Commit cf398b08 authored by Glenn Proctor's avatar Glenn Proctor
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misc-scripts/id_mapping/default.conf
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View file @ cf398b08
......@@ -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
......
misc-scripts/surgery/convert120_130.pl deleted 100644 → 0
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# 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();
misc-scripts/surgery/convert_6_main.pl deleted 100644 → 0
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View file @ 23991005
# 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();
misc-scripts/surgery/convert_7a_main.pl deleted 100644 → 0
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View file @ 23991005
# 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();
misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm
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View file @ cf398b08
......@@ -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 );
......
misc-scripts/xref_mapping/compare_mapping.pl
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......@@ -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
......
misc-scripts/xref_projection/project_display_xrefs.pl
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View file @ cf398b08
......@@ -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
......
misc-scripts/xref_projection/release_37.conf deleted 100644 → 0
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View file @ 23991005
#
# 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;
misc-scripts/xref_projection/release_38.conf deleted 100644 → 0
+ 0
− 288
View file @ 23991005
#
# 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;
misc-scripts/xref_projection/release_47.ini deleted 100644 → 0
+ 0
− 189
View file @ 23991005
; 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
misc-scripts/xref_projection/submit_projections.pl
+ 1
− 1
View file @ cf398b08
......@@ -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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