src/hg/makeDb/trackDb/trackDb.ra 1.520
1.520 2009/07/10 21:11:54 hiram
the ChainNet tracks should be specified by their db name
Index: src/hg/makeDb/trackDb/trackDb.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.ra,v
retrieving revision 1.519
retrieving revision 1.520
diff -b -B -U 4 -r1.519 -r1.520
--- src/hg/makeDb/trackDb/trackDb.ra 10 Jul 2009 06:21:04 -0000 1.519
+++ src/hg/makeDb/trackDb/trackDb.ra 10 Jul 2009 21:11:54 -0000 1.520
@@ -2094,8 +2094,46 @@
spectrum on
type netAlign tetNig1 chainTetNig1
otherDb tetNig1
+track danRer6ChainNet
+compositeTrack on
+shortLabel Zebrafish Chain/Net
+longLabel Zebrafish (Dec. 2008/danRer6), Chain and Net alignment tracks
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 159
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb galGal3
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+ track chainDanRer6
+ subTrack danRer6ChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain danRer6
+
+ track netDanRer6
+ subTrack danRer6ChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign danRer6 chainDanRer6
+
track chainDanRer5
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -2392,9 +2430,9 @@
type netAlign galGal2 chainGalGal2
otherDb galGal2
# release alpha until individual galGal3 tracks are obsolete
-track chickenChainNet
+track galGal3ChainNet
compositeTrack on
shortLabel Chicken Chain/Net
longLabel Chicken (May. 2006/galGal3), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -2418,16 +2456,16 @@
html chainNet
release alpha
track chainGalGal3
- subTrack chickenChainNet
+ subTrack galGal3ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain galGal3
track netGalGal3
- subTrack chickenChainNet
+ subTrack galGal3ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign galGal3 chainGalGal3
@@ -2545,9 +2583,9 @@
otherDb taeGut1
release beta
# release alpha until ornAna1 individual chain/net tracks phased out
-track platypusChainNet
+track ornAna1ChainNet
compositeTrack on
shortLabel Platypus Chain/Net
longLabel Platypus (Mar. 2007/ornAna1), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -2571,16 +2609,16 @@
html chainNet
release alpha
track chainOrnAna1
- subTrack platypusChainNet
+ subTrack ornAna1ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain ornAna1
track netOrnAna1
- subTrack platypusChainNet
+ subTrack ornAna1ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign ornAna1 chainOrnAna1
@@ -2633,9 +2671,9 @@
type netAlign macEug1 chainMacEug1
otherDb macEug1
# release alpha until monDom5 individual chain/net tracks phased out
-track opossumChainNet
+track monDom5ChainNet
compositeTrack on
shortLabel Opossum Chain/Net
longLabel Opossum (Oct. 2006/monDom5), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -2659,16 +2697,16 @@
html chainNet
release alpha
track chainMonDom5
- subTrack opossumChainNet
+ subTrack monDom5ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain monDom5
track netMonDom5
- subTrack opossumChainNet
+ subTrack monDom5ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign monDom5 chainMonDom5
@@ -2901,9 +2939,9 @@
type netAlign mm6 chainMm6
otherDb mm6
# release alpha until mm9 individual chain/net tracks phased out
-track mouseChainNet
+track mm9ChainNet
compositeTrack on
shortLabel Mouse Chain/Net
longLabel Mouse (Jul. 2007/mm9), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -2927,16 +2965,16 @@
html chainNet
release alpha
track chainMm9
- subTrack mouseChainNet
+ subTrack mm9ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain mm9
track netMm9
- subTrack mouseChainNet
+ subTrack mm9ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign mm9 chainMm9
@@ -3183,9 +3221,9 @@
type netAlign bosTau1 chainBosTau1
otherDb bosTau1
# release alpha until equCab1 phased out
-track horseChainNet
+track equCab2ChainNet
compositeTrack on
shortLabel Horse Chain/Net
longLabel Horse (Sep. 2007/equCab2), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -3209,23 +3247,23 @@
html chainNet
release alpha
track chainEquCab2
- subTrack horseChainNet
+ subTrack equCab2ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain equCab2
track netEquCab2
- subTrack horseChainNet
+ subTrack equCab2ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign equCab2 chainEquCab2
# release alpha until canFam2 individual tracks phased out
-track dogChainNet
+track canFam2ChainNet
compositeTrack on
shortLabel Dog Chain/Net
longLabel Dog (May 2005/canFam2), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -3249,16 +3287,16 @@
html chainNet
release alpha
track chainCanFam2
- subTrack dogChainNet
+ subTrack canFam2ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain canFam2
track netCanFam2
- subTrack dogChainNet
+ subTrack canFam2ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign canFam2 chainCanFam2
@@ -4642,9 +4680,9 @@
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign venter1 chainVenter1
otherDb venter1
-track humanChainNet
+track hg19ChainNet
compositeTrack on
shortLabel Human Chain/Net
longLabel Human (Feb. 2009/hg19), Chain and Net alignment tracks
subGroup1 view Views chain=Chain net=Net
@@ -4667,16 +4705,16 @@
html chainNet
release alpha
track chainHg19
- subTrack humanChainNet
+ subTrack hg19ChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain hg19
track netHg19
- subTrack humanChainNet
+ subTrack hg19ChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment net
type netAlign hg19 chainHg19