[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a8ae4ca2480/ Changeset: 8a8ae4ca2480 User: natefoo Date: 2014-02-27 22:37:48 Summary: Rename ucsc_build_sites.txt to .sample. Affected #: 4 files diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 run.sh --- a/run.sh +++ b/run.sh @@ -24,6 +24,7 @@ tool-data/shared/ensembl/builds.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/*.sample diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 tool-data/shared/ucsc/ucsc_build_sites.txt --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn -main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 -#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn -archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 -ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 diff -r 739287adeac8561c32d6dcf24d7eb9309d992da3 -r 8a8ae4ca248027a93bb536926004d1fc78032534 tool-data/shared/ucsc/ucsc_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt.sample @@ -0,0 +1,7 @@ +#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn +main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 +#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn +archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 +ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 https://bitbucket.org/galaxy/galaxy-central/commits/35105e993ae9/ Changeset: 35105e993ae9 User: natefoo Date: 2014-03-28 21:44:54 Summary: Merged in natefoo/galaxy-central (pull request #340) Rename ucsc_build_sites.txt to .sample. Affected #: 4 files diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e .hgignore --- a/.hgignore +++ b/.hgignore @@ -77,6 +77,7 @@ tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt tool-data/*.loc tool-data/genome/* diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e run.sh --- a/run.sh +++ b/run.sh @@ -24,6 +24,7 @@ tool-data/shared/ensembl/builds.txt.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/*.sample diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e tool-data/shared/ucsc/ucsc_build_sites.txt --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ /dev/null @@ -1,7 +0,0 @@ -#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn -main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 -#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn -archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 -#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn -test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 -ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 diff -r e78c9aa7dc4642a3ddac6696ce5c56c58b936443 -r 35105e993ae91da02eb222db3007541bd4de4c3e tool-data/shared/ucsc/ucsc_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt.sample @@ -0,0 +1,7 @@ +#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn +main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,hg19,felCat3,apiMel2,monDom4,apiMel1,ce2 +#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn +archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 +#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn +test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 +ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.