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synchronise against latest UCSC versions #3874

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merged 2 commits into from Apr 7, 2017

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commented Apr 5, 2017

This PR will update the builds.txt.sample and the ucsc_build_sites.txt.sample by running bash ./cron/updateucsc.sh.sample locally.

A few genomes simply do not exists at UCSC anymore and a few important one where missing.

@bgruening bgruening requested a review from blankenberg Apr 5, 2017

@galaxybot galaxybot added the triage label Apr 5, 2017

@galaxybot galaxybot added this to the 17.05 milestone Apr 5, 2017

#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
test http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? picPub1,megLyr1,caePb3,eptFus1,caeRem4,caeRem2,caeRem3,geoFor1,caeRem1,oryLat2,oryLat1,homIni13,homIni14,cacTus1,cacTus2,cacTus3,oryCun1,oryCun2,chlSab2,lepDis1,chlSab1,kirRefV3,kirRefV2,kirRefV5,kirRefV4,sc1,mhcRefnoNs8,mhcRefnoNs9,choHof1,poeRet1,mhcRefnoNs2,mhcRefnoNs3,mhcRefnoNs4,mhcRefnoNs5,mhcRefnoNs6,mhcRefnoNs7,resEbo1,cotJap1,ci2,simHumanPrim,pteVam1,venter1,priPac1,priPac2,priPac3,allSin1,eutHer13,aptMan1,nipNip1,bioGla0,phyCat1,mhcRefnoNs,equCab2,simHumanMammal,equCab1,rheMac7,rheMac3,rheMac2,simRefMam,rheMac8,colAng1,droVir2,droVir1,repBase0,repBase1,cypVar1,ornAna1,neoBri1,conCri1,droRho2,nemVec1,lotGig0,homIni20,poeFor1,phaLep1,droPse3,saiBol1,gliRes13,caeSp51,lauRas13,ailMel1,xenLae2,panTro5,panTro4,calAnn1,capHir1,panTro3,mm10,panTro2,plasFalc3D7V12,bubBub1,oncVol1,nonAfr13,fulGla1,apaVit1,colLiv1,apiMel1,zaiEbo1,apiMel2,apiMel4,serCan1,thaSir1,opiHoa1,droKik2,panTro1,cheMyd1,phaCar1,mhcRefnoNs12,hg19Patch10,pygAde1,halLeu1,afrOth13,caeSp71,melGal1,melGal5,gavGan0,equPrz1,angJap1,rhiFer1,araMac1,sebRub1,caeSp111,droBia2,tarSyr1,tarSyr2,aciBauTYTH_1,takFla1,chrPic2,chrPic1,amaVit1,criGri1,galVar1,oviAri3,papAnu2,ce6,ce5,ce4,ce3,ce2,chiLan1,ce9,ce8,priExs1,capCar1,egrGar1,droEug2,mesUni1,gadMor1,droAna1,droAna2,sacCer2,sacCer3,sacCer1,braNey38,ptePar1,ochPri2,melHap1,mm9,mm8,tarIhg38,mm7,pelSin1,myoLuc2,myoLuc1,rouAeg1,droPer1,balAcu1,euaGli13,melUnd1,marVir1,droSim1,aptFor1,necAme1,sebNig1,burXyl1,oviAri1,petMar1,petMar2,canFam2,dirImm1,carCri1,triSpi1,cioSav2,corBra1,cioSav1,caePb2,canFam1,canFam3,droSim2,caePb1,cucCan1,myoBra1,eboVir2,eboVir3,aquChr1,eboVir1,hg19Haps,cynSem1,mhcRefnoNs24,mhcRefnoNs23,mhcRefnoNs22,mhcRefnoNs21,mhcRefnoNs20,halAlb1,xenTro3,xenTro2,xenTro7,falPer1,droBip2,tauEry1,hg38Patch6,hg38Patch7,hg38Patch5,hg38Patch2,hg38Patch3,hg38,hg38Patch9,bisBis1,cavPor3,canHg12,aquChr2,mesAur1,tetNig2,bosTau8,tetNig1,pytBiv1,bruMal1,bosTau3,bosTau2,bosTau5,bosTau4,bosTau7,bosTau6,echTel1,oryAfe1,evoSim1,hetGla2,hetGla1,droMoj1,droMoj2,allMis1,allMis0,otoGar1,otoGar3,myoDav1,falChe1,bosMut1,acaChl1,droSuz1,anoGam1,punNye1,nanGal1,ornAna2,odoRosDiv1,oxyTri2,loxAfr1,loxAfr3,loxAfr2,dp3,dp2,astMex1,sorAra1,sorAra2,droMir2,taiEbo1,xenTro1,nasLar1,micOch1,caeJap1,ce7,caeJap3,caeJap2,taeGut1,caeJap4,taeGut2,mayZeb1,tupBel1,caeSp91,croPor0,hetBac1,ficAlb2,eidHel1,gorGor5,gorGor4,gorGor3,gorGor2,gorGor1,manPen1,micMur2,micMur3,micMur1,corCor1,proCap1,triSui1,mm10Strains1,xipMac1,eurHel1,chaVoc1,chaVoc2,pteGut1,hlaRef3,hlaRef2,hlaRef1,droYak1,oreNil2,lipVex1,droYak2,esoLuc1,rhiBie1,calJac1,macFas5,calJac3,colStr1,sudEbo1,danRer10,centromeres1,aplCal1,melInc1,melInc2,braFlo1,braFlo2,jacJac1,macNem1,simHumanMam,papHam1,ponAbe2,ce11,ce10,calMil1,calMil0,hapBur1,merNub1,falciparum,manVit1,fr3,fr2,fr1,gasAcu1,zonAlb1,tupChi1,mhcRefnoNs18,mhcRefnoNs19,lepOcu1,loaLoa1,panRed1,mhcRefnoNs13,mhcRefnoNs10,mhcRefnoNs11,mhcRefnoNs16,mhcRefnoNs17,mhcRefnoNs14,mhcRefnoNs15,balPav1,danRer7,danRer6,danRer5,danRer4,danRer3,eleEdw1,droEle2,musFur1,ochPri3,rodEnt13,monDom1,dm2,gavSte1,letCam1,latCha1,eriEur1,eriEur2,lepWed1,anoCar1,anoCar2,rn3,rn6,rn5,rn4,haeCon1,oreNil1,droYak3,haeCon2,mhcRef,vicPac1,vicPac2,bunEbo1,perManBai1,canFamPoodle1,droAlb1,tinGut2,tinGut1,strRat1,strRat2,droWil2,aplCal0,octDeg1,speTri1,bruMal2,CHM1,dasNov1,dasNov2,dasNov3,caeAng2,droTak2,speTri2,caeAng1,musDom2,panTig1,nanPar1,macEug1,galGal5,galGal4,galGal3,galGal2,droEre1,rhiRox1,anaPla1,mmtv,braNey1,sarHar1,panHod1,stePar1,ascSuu1,tytAlb1,turTru1,notCor1,camFer1,cerSim1,pelCri1,triMan1,hg15,hg16,hg17,hg18,hg19,ursMar1,monDom5,monDom4,pteAle1,panPan1,panPan2,droSec1,xenTro9,ancCey1,bucRhi1,susScr1,susScr2,susScr3,hg19LggInv,echTel2,strPur4,ci3,dm1,ci1,dm3,dm6,strCam1,pseHum1,mm10Patch1,mm10Patch4,droGri1,homPan20,macEug2,chlUnd1,nomLeu3,nomLeu2,nomLeu1,ecoRef1,ecoRef3,ecoRef2,chrAsi1,ecoRef4,apaSpi1,dicLab1,dipOrd1,hg19Patch2,hg19Patch5,hg19Patch9,priMat13,turTru2,repeats2,cb2,cb3,cb1,borEut13,cb4,felCat3,strPur1,strPur3,strPur2,droFic2,kirRef,phoRub1,felCat8,catArr1,orcOrc1,triCas2,felCat4,felCat5
ucla http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1

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nsoranzo Apr 6, 2017

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On my server I don't have this last line any more.

@bgruening

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commented Apr 7, 2017

Thanks @nsoranzo. I still had it on my older server.

@bgruening bgruening referenced this pull request Apr 7, 2017

Merged

Docker - RNA-seq #277

@nsoranzo nsoranzo merged commit 5b88069 into galaxyproject:dev Apr 7, 2017

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