src/hg/makeDb/schema/all.joiner 1.758

Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.757
retrieving revision 1.758
diff -b -B -U 4 -r1.757 -r1.758
--- src/hg/makeDb/schema/all.joiner	4 Jan 2010 22:39:19 -0000	1.757
+++ src/hg/makeDb/schema/all.joiner	7 Jan 2010 00:09:35 -0000	1.758
@@ -82,17 +82,17 @@
 set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
 
 # Define transMap databases
 # transMapDb not public: dasNov1,echTel1,loxAfr1,oryCun1,otoGar1,loxAfr3
-set transMapDb anoCar1,bosTau4,calJac1,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,xenTro2
+set transMapDb anoCar1,bosTau4,calJac1,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2
 
 # Set up list of databases we ignore and those we check.  Program
 # will complain about other databases.
 databasesChecked $gbd,$otherDb
 databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash
 
 # Define various non-self chains
-set chainDest Hg16,Hg17,Hg18,Hg19,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr3
+set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr3
 
 # Define databases that support known genes
 set kgDb $hg,$mm,$rn
 # Older format (KG 2)
@@ -1074,8 +1074,12 @@
     hg19.chain[].id
     hg19.chain[]Link.chainId full
     hg19.net[].chainId exclude=0
     hg19.netSynteny[].chainId exclude=0
+    $tetNig.chain[].id
+    $tetNig.chain[]Link.chainId full
+    $tetNig.net[].chainId exclude=0
+    $tetNig.netSynteny[].chainId exclude=0
 
 identifier rBestChainPanTro1Id
 "Link together reciprocal best chain/net"
     hg16.rBestChainPanTro1.id $split
@@ -1900,8 +1904,13 @@
     $gbd.ensEstGene.name chopAfter=.
     $gbd.ensEstGtp.transcript chopAfter=.
     $gbd.ensEstPep.name chopAfter=.
 
+identifier gazeGeneId external=Genoscope
+"GAZE Gene ID"
+    $gbd.gaze.name
+    $gbd.gazePep.name
+
 # H-Invitational Database Identifiers
 
 identifier hinvTranscriptId external=H-INV dependency
 "H-Invitational Transcript ID"
@@ -3448,9 +3457,9 @@
     uwFootprintsPrints
     uwFootprintsTagCounts
 
 tablesIgnored $tetNig
-    gaze
+    gold
     ecoresHg17
     cytokines
     hoxGenes