From 8a41c440ebe98f7f1cec677239f0df62dc3fd1be Mon Sep 17 00:00:00 2001 From: TamaraNaboulsi Date: Thu, 30 Oct 2025 13:09:13 +0000 Subject: [PATCH 1/3] New and removed genomes for release 116 --- conf/SiteDefs.pm | 35 ++++++++-------- ... => bactrocera_oleae_gca042242935v1rs.ini} | 0 conf/ini-files/caenorhabditis_remanei.ini | 40 ------------------- ...erax_quadricarinatus_gca038502225v1rs.ini} | 2 +- ... => daphnia_carinata_gca022539665v4rs.ini} | 0 ...dermacentor_andersoni_gca023375885v3rs.ini | 19 +++++++++ conf/ini-files/drosophila_pseudoobscura.ini | 38 ------------------ ...> drosophila_suzukii_gca043229965v1rs.ini} | 2 +- ...i => hyalella_azteca_gca000764305v4rs.ini} | 0 ...eophtheirus_salmonis_gca016086655v5rs.ini} | 0 ...otrombidium_deliense_gca003675905v2gb.ini} | 0 ...085v1.ini => loa_loa_gca000183805v3rs.ini} | 0 ...> neodiprion_pinetum_gca021155775v2rs.ini} | 0 ...> onthophagus_taurus_gca036711975v1rs.ini} | 2 +- ...rasteatoda_tepidariorum_gca000365465v3.ini | 22 ---------- ...teatoda_tepidariorum_gca043381705v1rs.ini} | 2 +- .../patella_vulgata_gca932274485v2rs.ini | 22 ++++++++++ .../penaeus_vannamei_gca042767895v1rs.ini | 22 ++++++++++ ...plodia_interpunctella_gca027563975v2rs.ini | 22 ++++++++++ ...ollicipes_pollicipes_gca011947565v3rs.ini} | 0 ...ristionchus_pacificus_gca000180635v4gb.ini | 22 ++++++++++ ... procambarus_clarkii_gca040958095v1rs.ini} | 0 .../stylophora_pistillata_gca002571385v1.ini | 22 ---------- 23 files changed, 129 insertions(+), 143 deletions(-) rename conf/ini-files/{lytechinus_pictus_gca015342785v2rs.ini => bactrocera_oleae_gca042242935v1rs.ini} (100%) delete mode 100755 conf/ini-files/caenorhabditis_remanei.ini rename conf/ini-files/{mercenaria_mercenaria_gca014805675v2.ini => cherax_quadricarinatus_gca038502225v1rs.ini} (89%) rename conf/ini-files/{schistosoma_haematobium_gca000699445v2rs.ini => daphnia_carinata_gca022539665v4rs.ini} (100%) create mode 100644 conf/ini-files/dermacentor_andersoni_gca023375885v3rs.ini delete mode 100644 conf/ini-files/drosophila_pseudoobscura.ini rename conf/ini-files/{cherax_quadricarinatus_gca026875155v2rs.ini => drosophila_suzukii_gca043229965v1rs.ini} (89%) rename conf/ini-files/{hyalella_azteca_gca000764305v2.ini => hyalella_azteca_gca000764305v4rs.ini} (100%) rename conf/ini-files/{hydra_vulgaris_gca022113875v1rs.ini => lepeophtheirus_salmonis_gca016086655v5rs.ini} (100%) rename conf/ini-files/{necator_americanus.ini => leptotrombidium_deliense_gca003675905v2gb.ini} (100%) rename conf/ini-files/{penaeus_vannamei_gca003789085v1.ini => loa_loa_gca000183805v3rs.ini} (100%) rename conf/ini-files/{procambarus_clarkii_gca020424385v2.ini => neodiprion_pinetum_gca021155775v2rs.ini} (100%) rename conf/ini-files/{ostrea_edulis_gca023158985v1rs.ini => onthophagus_taurus_gca036711975v1rs.ini} (89%) delete mode 100644 conf/ini-files/parasteatoda_tepidariorum_gca000365465v3.ini rename conf/ini-files/{eufriesea_mexicana_gca001483705v1rs.ini => parasteatoda_tepidariorum_gca043381705v1rs.ini} (89%) create mode 100644 conf/ini-files/patella_vulgata_gca932274485v2rs.ini create mode 100644 conf/ini-files/penaeus_vannamei_gca042767895v1rs.ini create mode 100644 conf/ini-files/plodia_interpunctella_gca027563975v2rs.ini rename conf/ini-files/{lepeophtheirus_salmonis_gca016086655v3rs.ini => pollicipes_pollicipes_gca011947565v3rs.ini} (100%) create mode 100644 conf/ini-files/pristionchus_pacificus_gca000180635v4gb.ini rename conf/ini-files/{pollicipes_pollicipes_gca011947565v2.ini => procambarus_clarkii_gca040958095v1rs.ini} (100%) delete mode 100644 conf/ini-files/stylophora_pistillata_gca002571385v1.ini diff --git a/conf/SiteDefs.pm b/conf/SiteDefs.pm index 343ed08..c3f4414 100755 --- a/conf/SiteDefs.pm +++ b/conf/SiteDefs.pm @@ -91,6 +91,7 @@ sub update_conf { bactrocera_latifrons_gca001853355v1 bactrocera_neohumeralis_gca024586455v2rs bactrocera_oleae_gca001188975v4rs + bactrocera_oleae_gca042242935v1rs bactrocera_tryoni_gca016617805v2 belgica_antarctica bemisia_tabaci_asiaii5 @@ -116,7 +117,6 @@ sub update_conf { caenorhabditis_briggsae caenorhabditis_elegans caenorhabditis_japonica - caenorhabditis_remanei caenorhabditis_remanei_gca010183535v1rs camponotus_floridanus_gca003227725v1rs capitella_teleta @@ -124,7 +124,7 @@ sub update_conf { centruroides_sculpturatus_gca000671375v2 ceratitis_capitata_gca000347755v4 chelonus_insularis_gca013357705v1rs - cherax_quadricarinatus_gca026875155v2rs + cherax_quadricarinatus_gca038502225v1rs chrysoperla_carnea_gca905475395v1rs cimex_lectularius clytia_hemisphaerica_gca902728285 @@ -146,12 +146,14 @@ sub update_conf { danaus_plexippus danaus_plexippus_gca018135715v1 daphnia_carinata_gca022539665v3rs + daphnia_carinata_gca022539665v4rs daphnia_magna_gca020631705v2 daphnia_pulex_gca021134715v1rs daphnia_pulicaria_gca021234035v2rs dendroctonus_ponderosae_gca020466585v2rs dendronephthya_gigantea_gca004324835v1 dermacentor_andersoni_gca023375885v2rs + dermacentor_andersoni_gca023375885v3rs dermacentor_silvarum_gca013339745v2rs dermatophagoides_pteronyssinus_gca001901225v2 diabrotica_virgifera_gca917563875v2rs @@ -188,7 +190,6 @@ sub update_conf { drosophila_novamexicana_gca003285875v3rs drosophila_obscura_gca018151105v1rs drosophila_persimilis_gca003286085v2rs - drosophila_pseudoobscura drosophila_pseudoobscura_gca009870125v2rs drosophila_rhopaloa_gca018152115v1rs drosophila_santomea_gca016746245v2rs @@ -199,6 +200,7 @@ sub update_conf { drosophila_subpulchrella_gca014743375v2rs drosophila_sulfurigaster_gca023558435v2rs drosophila_suzukii_gca037355615v1rs + drosophila_suzukii_gca043229965v1rs drosophila_takahashii_gca030179915v2rs drosophila_teissieri_gca016746235v2rs drosophila_tropicalis_gca018151085v1rs @@ -208,7 +210,6 @@ sub update_conf { dufourea_novaeangliae_gca001272555v1rs echinococcus_granulosus_gca000524195v1rs eriocheir_sinensis_gca024679095v1rs - eufriesea_mexicana_gca001483705v1rs eufriesea_mexicana_gca001483705v2rs eurytemora_carolleeae_gca000591075v1rs exaiptasia_diaphana_gca001417965v1 @@ -239,9 +240,8 @@ sub update_conf { homalodisca_vitripennis_gca021130785v2rs homarus_americanus_gca018991925v1 homarus_gammarus_gca958450375v1 - hyalella_azteca_gca000764305v2 + hyalella_azteca_gca000764305v4rs hyalomma_asiaticum_gca013339685v2vb - hydra_vulgaris_gca022113875v1rs hydra_vulgaris_gca038396675v1rs hydractinia_symbiolongicarpus_gca029227915v2rs hylaeus_anthracinus_gca026225885v1rs @@ -254,9 +254,10 @@ sub update_conf { ixodes_scapularis_gca016920785v2 ixodes_scapularis_ise6 leguminivora_glycinivorella_gca023078275v1rs - lepeophtheirus_salmonis_gca016086655v3rs + lepeophtheirus_salmonis_gca016086655v5rs leptinotarsa_decemlineata_gca000500325v2 leptotrombidium_deliense + leptotrombidium_deliense_gca003675905v2gb limnephilus_lunatus_gca917563855v2 limnephilus_marmoratus_gca917880885v1 limnephilus_rhombicus_gca929108145v2 @@ -267,13 +268,13 @@ sub update_conf { lingula_anatina_gca001039355v2 liolophura_japonica_gca032854445v1rs loa_loa + loa_loa_gca000183805v3rs lottia_gigantea lucilia_cuprina lucilia_cuprina_gca022045245v1rs lucilia_sericata_gca015586225v1rs lutzomyia_longipalpis lutzomyia_longipalpis_gca024334085v1rs - lytechinus_pictus_gca015342785v2rs lytechinus_pictus_gca037042905v1rs lytechinus_variegatus_gca018143015v1 machimus_atricapillus_gca933228815v1 @@ -287,7 +288,6 @@ sub update_conf { megaselia_scalaris melanaphis_sacchari_gca002803265v2rs melitaea_cinxia_gca905220565v1 - mercenaria_mercenaria_gca014805675v2 mercenaria_mercenaria_gca021730395v1rs microctonus_aethiopoides_gca030272655v1cm microctonus_aethiopoides_gca030272935v1cm @@ -303,31 +303,32 @@ sub update_conf { myopa_tessellatipennis_gca943737955v2 mytilus_californianus_gca021869535v1rs nasonia_vitripennis - necator_americanus necator_americanus_gca031761385v1rs nematostella_vectensis nematostella_vectensis_gca932526225v1rs neodiprion_lecontei_gca021901455v1rs neodiprion_pinetum_gca021155775v1rs + neodiprion_pinetum_gca021155775v2rs nilaparvata_lugens_gca014356525v1rs octopus_bimaculoides_gca001194135v2rs octopus_sinensis_gca006345805v1 onchocerca_volvulus onthophagus_taurus_gca000648695v2 + onthophagus_taurus_gca036711975v1rs ooceraea_biroi_gca003672135v1 oppia_nitens_gca028296485v1rs orbicella_faveolata_gca002042975v1 orchesella_cincta ornithodoros_turicata_gca037126465v1rs orussus_abietinus_gca000612105v2 - ostrea_edulis_gca023158985v1rs ostrea_edulis_gca947568905v1rs owenia_fusiformis_gca903813345v1 panonychus_citri_gca014898815v1rs paramacrobiotus_metropolitanus_gca019649055v1rs - parasteatoda_tepidariorum_gca000365465v3 + parasteatoda_tepidariorum_gca043381705v1rs patella_pellucida_gca917208275v1 patella_vulgata_gca932274485v1 + patella_vulgata_gca932274485v2rs patiria_miniata_gca015706575v1 pecten_maximus_gca902652985v1rs pectinophora_gossypiella_gca024362695v1rs @@ -335,7 +336,7 @@ sub update_conf { penaeus_chinensis_gca019202785v2rs penaeus_japonicus_gca017312705v1 penaeus_monodon_gca015228065v1 - penaeus_vannamei_gca003789085v1 + penaeus_vannamei_gca042767895v1rs phlebotomus_argentipes_gca947086385v1rs phlebotomus_papatasi phlebotomus_papatasi_gca024763615v2rs @@ -343,18 +344,20 @@ sub update_conf { photinus_pyralis_gca008802855v1rs platynereis_dumerilii_gca026936325v1cm plodia_interpunctella_gca027563975v1rs + plodia_interpunctella_gca027563975v2rs pocillopora_damicornis_gca003704095v1 pogonomyrmex_barbatus_gca000187915v1rs polistes_canadensis_gca001313835v1rs polistes_dominula_gca001465965v1rs polistes_fuscatus_gca010416935v1rs - pollicipes_pollicipes_gca011947565v2 + pollicipes_pollicipes_gca011947565v3rs pomacea_canaliculata_gca003073045v1 pomphorhynchus_laevis_gca012934845v2gb portunus_trituberculatus_gca017591435v1 priapulus_caudatus_gca000485595v2 pristionchus_pacificus - procambarus_clarkii_gca020424385v2 + pristionchus_pacificus_gca000180635v4gb + procambarus_clarkii_gca040958095v1rs rhagoletis_pomonella_gca013731165v1 rhipicephalus_microplus_gca013339725v1 rhipicephalus_sanguineus_gca013339695v2rs @@ -369,7 +372,6 @@ sub update_conf { schistocerca_nitens_gca023898315v2rs schistocerca_piceifrons_gca021461385v2rs schistocerca_serialis_gca023864345v3rs - schistosoma_haematobium_gca000699445v2rs schistosoma_haematobium_gca000699445v3rs schistosoma_mansoni schmidtea_mediterranea_gca045838255v1cm @@ -387,7 +389,6 @@ sub update_conf { strigamia_maritima strongylocentrotus_purpuratus strongyloides_ratti - stylophora_pistillata_gca002571385v1 stylophora_pistillata_gca002571385v2 teleopsis_dalmanni tenebrio_molitor_gca907166875v3gb diff --git a/conf/ini-files/lytechinus_pictus_gca015342785v2rs.ini b/conf/ini-files/bactrocera_oleae_gca042242935v1rs.ini similarity index 100% rename from conf/ini-files/lytechinus_pictus_gca015342785v2rs.ini rename to conf/ini-files/bactrocera_oleae_gca042242935v1rs.ini diff --git a/conf/ini-files/caenorhabditis_remanei.ini b/conf/ini-files/caenorhabditis_remanei.ini deleted file mode 100755 index daec822..0000000 --- a/conf/ini-files/caenorhabditis_remanei.ini +++ /dev/null @@ -1,40 +0,0 @@ -[general] -ENSEMBL_GENOME_SIZE = 0.03 -DATA_SOURCE = WormBase (www.wormbase.org) -DB_BUILDER = WormBase -SPECIES_RELEASE_VERSION = 279 - - -[databases] - - -[ENSEMBL_STYLE] - -[EXTERNAL_GENOME_BROWSERS] -EGB_WORMBASE = WormBase browser - -#################### -# Configure External URLs -# These are mainly for (1) External Genome Browse {EGB_ } -# (2) DAS tracks {DAS_ } -#################### - -[ENSEMBL_EXTERNAL_URLS] -EGB_WORMBASE = http://www.wormbase.org/db/gb2/gbrowse/c_remanei/?name=###CHR###%3A###START###..###END### -WORMBASE_GENE = http://www.wormbase.org/species/c_remanei/gene/###ID### -WORMBASE_LOCUS = http://www.wormbase.org/species/c_remanei/gene/###ID### -WORMBASE_GSEQNAME = http://www.wormbase.org/species/c_remanei/gene/###ID### -WORMBASE_TRANSCRIPT = http://www.wormbase.org/species/c_remanei/transcript/###ID#### -WORMPEP_ID = http://www.wormbase.org/species/c_remanei/protein/RP:###ID### - -[ENSEMBL_INTERNAL_DAS_SOURCES] - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - -[ENSEMBL_EXTERNAL_DATABASES] - -[ENSEMBL_EXTERNAL_INDEXERS] - -coords = [ wormbase_gene ] diff --git a/conf/ini-files/mercenaria_mercenaria_gca014805675v2.ini b/conf/ini-files/cherax_quadricarinatus_gca038502225v1rs.ini similarity index 89% rename from conf/ini-files/mercenaria_mercenaria_gca014805675v2.ini rename to conf/ini-files/cherax_quadricarinatus_gca038502225v1rs.ini index b9c7823..26125e2 100644 --- a/conf/ini-files/mercenaria_mercenaria_gca014805675v2.ini +++ b/conf/ini-files/cherax_quadricarinatus_gca038502225v1rs.ini @@ -3,7 +3,7 @@ SPECIES_RELEASE_VERSION = 1 -ENSEMBL_GENOME_SIZE = 0.5 +ENSEMBL_GENOME_SIZE = 0.4 [ENSEMBL_STYLE] diff --git a/conf/ini-files/schistosoma_haematobium_gca000699445v2rs.ini b/conf/ini-files/daphnia_carinata_gca022539665v4rs.ini similarity index 100% rename from conf/ini-files/schistosoma_haematobium_gca000699445v2rs.ini rename to conf/ini-files/daphnia_carinata_gca022539665v4rs.ini diff --git a/conf/ini-files/dermacentor_andersoni_gca023375885v3rs.ini b/conf/ini-files/dermacentor_andersoni_gca023375885v3rs.ini new file mode 100644 index 0000000..2298cd7 --- /dev/null +++ b/conf/ini-files/dermacentor_andersoni_gca023375885v3rs.ini @@ -0,0 +1,19 @@ + +[general] + +SPECIES_RELEASE_VERSION = 1 + +[ENSEMBL_STYLE] + +[ENSEMBL_COLOURS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + \ No newline at end of file diff --git a/conf/ini-files/drosophila_pseudoobscura.ini b/conf/ini-files/drosophila_pseudoobscura.ini deleted file mode 100644 index 05322e8..0000000 --- a/conf/ini-files/drosophila_pseudoobscura.ini +++ /dev/null @@ -1,38 +0,0 @@ -[general] -SPECIES_RELEASE_VERSION = 4 -ENSEMBL_GENOME_SIZE = 0.07 -DB_BUILDER = FlyBase -UCSC_GOLDEN_PATH = dp3 - -# Search config -ENSEMBL_SEARCH_IDXS = [ Domain Family Gene GenomicAlignment Sequence ] - -[databases] - - -[ENSEMBL_STYLE] - -[EXTERNAL_GENOME_BROWSERS] -EGB_FLYBASE = FlyBase browser - -#################### -# Configure External URLs -# These are mainly for (1) External Genome Browse {EGB_ } -# (2) DAS tracks {DAS_ } -#################### - -[ENSEMBL_EXTERNAL_URLS] -EGB_FLYBASE = http://flybase.org/cgi-bin/gbrowse/dpse/?name=###CHR###%3A###START###..###END### - -[ENSEMBL_INTERNAL_DAS_SOURCES] - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - -[ENSEMBL_EXTERNAL_DATABASES] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini - -[ENSEMBL_EXTERNAL_INDEXERS] -; DO NOT REMOVE THIS HEADER - defined in DEFAULTS.ini - diff --git a/conf/ini-files/cherax_quadricarinatus_gca026875155v2rs.ini b/conf/ini-files/drosophila_suzukii_gca043229965v1rs.ini similarity index 89% rename from conf/ini-files/cherax_quadricarinatus_gca026875155v2rs.ini rename to conf/ini-files/drosophila_suzukii_gca043229965v1rs.ini index 5dd13c0..26125e2 100644 --- a/conf/ini-files/cherax_quadricarinatus_gca026875155v2rs.ini +++ b/conf/ini-files/drosophila_suzukii_gca043229965v1rs.ini @@ -3,7 +3,7 @@ SPECIES_RELEASE_VERSION = 1 -ENSEMBL_GENOME_SIZE = 0.6 +ENSEMBL_GENOME_SIZE = 0.4 [ENSEMBL_STYLE] diff --git a/conf/ini-files/hyalella_azteca_gca000764305v2.ini b/conf/ini-files/hyalella_azteca_gca000764305v4rs.ini similarity index 100% rename from conf/ini-files/hyalella_azteca_gca000764305v2.ini rename to conf/ini-files/hyalella_azteca_gca000764305v4rs.ini diff --git a/conf/ini-files/hydra_vulgaris_gca022113875v1rs.ini b/conf/ini-files/lepeophtheirus_salmonis_gca016086655v5rs.ini similarity index 100% rename from conf/ini-files/hydra_vulgaris_gca022113875v1rs.ini rename to conf/ini-files/lepeophtheirus_salmonis_gca016086655v5rs.ini diff --git a/conf/ini-files/necator_americanus.ini b/conf/ini-files/leptotrombidium_deliense_gca003675905v2gb.ini similarity index 100% rename from conf/ini-files/necator_americanus.ini rename to conf/ini-files/leptotrombidium_deliense_gca003675905v2gb.ini diff --git a/conf/ini-files/penaeus_vannamei_gca003789085v1.ini b/conf/ini-files/loa_loa_gca000183805v3rs.ini similarity index 100% rename from conf/ini-files/penaeus_vannamei_gca003789085v1.ini rename to conf/ini-files/loa_loa_gca000183805v3rs.ini diff --git a/conf/ini-files/procambarus_clarkii_gca020424385v2.ini b/conf/ini-files/neodiprion_pinetum_gca021155775v2rs.ini similarity index 100% rename from conf/ini-files/procambarus_clarkii_gca020424385v2.ini rename to conf/ini-files/neodiprion_pinetum_gca021155775v2rs.ini diff --git a/conf/ini-files/ostrea_edulis_gca023158985v1rs.ini b/conf/ini-files/onthophagus_taurus_gca036711975v1rs.ini similarity index 89% rename from conf/ini-files/ostrea_edulis_gca023158985v1rs.ini rename to conf/ini-files/onthophagus_taurus_gca036711975v1rs.ini index b9c7823..bf46c00 100644 --- a/conf/ini-files/ostrea_edulis_gca023158985v1rs.ini +++ b/conf/ini-files/onthophagus_taurus_gca036711975v1rs.ini @@ -3,7 +3,7 @@ SPECIES_RELEASE_VERSION = 1 -ENSEMBL_GENOME_SIZE = 0.5 +ENSEMBL_GENOME_SIZE = 0.2 [ENSEMBL_STYLE] diff --git a/conf/ini-files/parasteatoda_tepidariorum_gca000365465v3.ini b/conf/ini-files/parasteatoda_tepidariorum_gca000365465v3.ini deleted file mode 100644 index 5a453f1..0000000 --- a/conf/ini-files/parasteatoda_tepidariorum_gca000365465v3.ini +++ /dev/null @@ -1,22 +0,0 @@ - -[general] - -SPECIES_RELEASE_VERSION = 1 - -ENSEMBL_GENOME_SIZE = 0.03 - - -[ENSEMBL_STYLE] - -[ENSEMBL_COLOURS] - -[ENSEMBL_EXTERNAL_URLS] - -[ENSEMBL_EXTERNAL_DATABASES] - -[ENSEMBL_EXTERNAL_INDEXERS] - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - \ No newline at end of file diff --git a/conf/ini-files/eufriesea_mexicana_gca001483705v1rs.ini b/conf/ini-files/parasteatoda_tepidariorum_gca043381705v1rs.ini similarity index 89% rename from conf/ini-files/eufriesea_mexicana_gca001483705v1rs.ini rename to conf/ini-files/parasteatoda_tepidariorum_gca043381705v1rs.ini index e1d4695..26125e2 100644 --- a/conf/ini-files/eufriesea_mexicana_gca001483705v1rs.ini +++ b/conf/ini-files/parasteatoda_tepidariorum_gca043381705v1rs.ini @@ -3,7 +3,7 @@ SPECIES_RELEASE_VERSION = 1 -ENSEMBL_GENOME_SIZE = 0.02 +ENSEMBL_GENOME_SIZE = 0.4 [ENSEMBL_STYLE] diff --git a/conf/ini-files/patella_vulgata_gca932274485v2rs.ini b/conf/ini-files/patella_vulgata_gca932274485v2rs.ini new file mode 100644 index 0000000..26125e2 --- /dev/null +++ b/conf/ini-files/patella_vulgata_gca932274485v2rs.ini @@ -0,0 +1,22 @@ + +[general] + +SPECIES_RELEASE_VERSION = 1 + +ENSEMBL_GENOME_SIZE = 0.4 + + +[ENSEMBL_STYLE] + +[ENSEMBL_COLOURS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + \ No newline at end of file diff --git a/conf/ini-files/penaeus_vannamei_gca042767895v1rs.ini b/conf/ini-files/penaeus_vannamei_gca042767895v1rs.ini new file mode 100644 index 0000000..bf46c00 --- /dev/null +++ b/conf/ini-files/penaeus_vannamei_gca042767895v1rs.ini @@ -0,0 +1,22 @@ + +[general] + +SPECIES_RELEASE_VERSION = 1 + +ENSEMBL_GENOME_SIZE = 0.2 + + +[ENSEMBL_STYLE] + +[ENSEMBL_COLOURS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + \ No newline at end of file diff --git a/conf/ini-files/plodia_interpunctella_gca027563975v2rs.ini b/conf/ini-files/plodia_interpunctella_gca027563975v2rs.ini new file mode 100644 index 0000000..f274cf8 --- /dev/null +++ b/conf/ini-files/plodia_interpunctella_gca027563975v2rs.ini @@ -0,0 +1,22 @@ + +[general] + +SPECIES_RELEASE_VERSION = 1 + +ENSEMBL_GENOME_SIZE = 0.05 + + +[ENSEMBL_STYLE] + +[ENSEMBL_COLOURS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + \ No newline at end of file diff --git a/conf/ini-files/lepeophtheirus_salmonis_gca016086655v3rs.ini b/conf/ini-files/pollicipes_pollicipes_gca011947565v3rs.ini similarity index 100% rename from conf/ini-files/lepeophtheirus_salmonis_gca016086655v3rs.ini rename to conf/ini-files/pollicipes_pollicipes_gca011947565v3rs.ini diff --git a/conf/ini-files/pristionchus_pacificus_gca000180635v4gb.ini b/conf/ini-files/pristionchus_pacificus_gca000180635v4gb.ini new file mode 100644 index 0000000..bf46c00 --- /dev/null +++ b/conf/ini-files/pristionchus_pacificus_gca000180635v4gb.ini @@ -0,0 +1,22 @@ + +[general] + +SPECIES_RELEASE_VERSION = 1 + +ENSEMBL_GENOME_SIZE = 0.2 + + +[ENSEMBL_STYLE] + +[ENSEMBL_COLOURS] + +[ENSEMBL_EXTERNAL_URLS] + +[ENSEMBL_EXTERNAL_DATABASES] + +[ENSEMBL_EXTERNAL_INDEXERS] + +[ENSEMBL_SPECIES_SITE] + +[SPECIES_DISPLAY_NAME] + \ No newline at end of file diff --git a/conf/ini-files/pollicipes_pollicipes_gca011947565v2.ini b/conf/ini-files/procambarus_clarkii_gca040958095v1rs.ini similarity index 100% rename from conf/ini-files/pollicipes_pollicipes_gca011947565v2.ini rename to conf/ini-files/procambarus_clarkii_gca040958095v1rs.ini diff --git a/conf/ini-files/stylophora_pistillata_gca002571385v1.ini b/conf/ini-files/stylophora_pistillata_gca002571385v1.ini deleted file mode 100644 index b88de2c..0000000 --- a/conf/ini-files/stylophora_pistillata_gca002571385v1.ini +++ /dev/null @@ -1,22 +0,0 @@ - -[general] - -SPECIES_RELEASE_VERSION = 1 - -ENSEMBL_GENOME_SIZE = 0.01 - - -[ENSEMBL_STYLE] - -[ENSEMBL_COLOURS] - -[ENSEMBL_EXTERNAL_URLS] - -[ENSEMBL_EXTERNAL_DATABASES] - -[ENSEMBL_EXTERNAL_INDEXERS] - -[ENSEMBL_SPECIES_SITE] - -[SPECIES_DISPLAY_NAME] - \ No newline at end of file From 6120774ac79cadc633d51027fd9d2080fbb83c8b Mon Sep 17 00:00:00 2001 From: TamaraNaboulsi Date: Thu, 6 Nov 2025 12:21:33 +0000 Subject: [PATCH 2/3] Add renamed genomes --- conf/SiteDefs.pm | 4 ++-- ...0696795v2rs.ini => halyomorpha_halys_gca000696795v3rs.ini} | 0 ...903813345v1.ini => owenia_fusiformis_gca903813345v2gb.ini} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename conf/ini-files/{halyomorpha_halys_gca000696795v2rs.ini => halyomorpha_halys_gca000696795v3rs.ini} (100%) rename conf/ini-files/{owenia_fusiformis_gca903813345v1.ini => owenia_fusiformis_gca903813345v2gb.ini} (100%) diff --git a/conf/SiteDefs.pm b/conf/SiteDefs.pm index c3f4414..3d8675f 100755 --- a/conf/SiteDefs.pm +++ b/conf/SiteDefs.pm @@ -229,7 +229,7 @@ sub update_conf { halichondria_panicea_gca963675165v1rs haliotis_rubra_gca003918875v1rs haliotis_rufescens_gca023055435v1rs - halyomorpha_halys_gca000696795v2rs + halyomorpha_halys_gca000696795v3rs harpegnathos_saltator_gca003227715v2rs heliconius_melpomene helicoverpa_armigera_gca030705265v1rs @@ -322,7 +322,7 @@ sub update_conf { ornithodoros_turicata_gca037126465v1rs orussus_abietinus_gca000612105v2 ostrea_edulis_gca947568905v1rs - owenia_fusiformis_gca903813345v1 + owenia_fusiformis_gca903813345v2gb panonychus_citri_gca014898815v1rs paramacrobiotus_metropolitanus_gca019649055v1rs parasteatoda_tepidariorum_gca043381705v1rs diff --git a/conf/ini-files/halyomorpha_halys_gca000696795v2rs.ini b/conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini similarity index 100% rename from conf/ini-files/halyomorpha_halys_gca000696795v2rs.ini rename to conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini diff --git a/conf/ini-files/owenia_fusiformis_gca903813345v1.ini b/conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini similarity index 100% rename from conf/ini-files/owenia_fusiformis_gca903813345v1.ini rename to conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini From 4f90ca07b9da4b02e1fe3db32ded0d4d8805c978 Mon Sep 17 00:00:00 2001 From: TamaraNaboulsi Date: Thu, 6 Nov 2025 12:39:04 +0000 Subject: [PATCH 3/3] Update release number for renamed genomes --- conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini | 4 ++-- conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini b/conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini index b88de2c..2072a5b 100644 --- a/conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini +++ b/conf/ini-files/halyomorpha_halys_gca000696795v3rs.ini @@ -1,7 +1,7 @@ [general] -SPECIES_RELEASE_VERSION = 1 +SPECIES_RELEASE_VERSION = 2 ENSEMBL_GENOME_SIZE = 0.01 @@ -19,4 +19,4 @@ ENSEMBL_GENOME_SIZE = 0.01 [ENSEMBL_SPECIES_SITE] [SPECIES_DISPLAY_NAME] - \ No newline at end of file + diff --git a/conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini b/conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini index bf46c00..1e0b14e 100644 --- a/conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini +++ b/conf/ini-files/owenia_fusiformis_gca903813345v2gb.ini @@ -1,7 +1,7 @@ [general] -SPECIES_RELEASE_VERSION = 1 +SPECIES_RELEASE_VERSION = 2 ENSEMBL_GENOME_SIZE = 0.2 @@ -19,4 +19,4 @@ ENSEMBL_GENOME_SIZE = 0.2 [ENSEMBL_SPECIES_SITE] [SPECIES_DISPLAY_NAME] - \ No newline at end of file +