3148a2ad3b931f8f9b8412b698ee20a48dd4c391
hiram
  Tue Aug 23 14:10:38 2022 -0700
adding lastz/chain/net Asiatic elephant GCF_024166365.1 to hg38 per user request refs #29905

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
index 19aeb26..e6b6e57 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
@@ -59,51 +59,53 @@
     track mafNetGCA_009914755.4Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCA_009914755.4
 
         track netGCA_009914755.4
         parent mafNetGCA_009914755.4Viewnet
         subGroups view=net
         shortLabel CHM13 T2T mafNet
         longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.summary.bb
         speciesOrder GCA_009914755.4
-        html chainNet
+        speciesLabels GCA_009914755.4="CHM13 T2T"
 
         track synNetGCA_009914755.4
         parent mafNetGCA_009914755.4Viewnet
         subGroups view=net
         shortLabel CHM13 T2T mafNet
         longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.summary.bb
         speciesOrder GCA_009914755.4
+        speciesLabels GCA_009914755.4="CHM13 T2T"
 
         track rbestNetGCA_009914755.4
         parent mafNetGCA_009914755.4Viewnet
         subGroups view=net
         shortLabel CHM13 T2T mafNet
         longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.summary.bb
         speciesOrder GCA_009914755.4
+        speciesLabels GCA_009914755.4="CHM13 T2T"
 
 ##############################################################################
 # GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal
 ##############################################################################
 track chainNetGCA_901343595v1
 compositeTrack on
 shortLabel $o_Organism Chain/Net
 longLabel $o_Organism ($o_date), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 200.3
 color 0,0,0
@@ -119,45 +121,43 @@
 html chainNet
 
     track chainNetGCA_901343595v1Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCA_901343595v1
     spectrum on
 
         track chainGCA_901343595v1_MONAX5
         parent chainNetGCA_901343595v1Viewchain
         subGroups view=chain
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
         type chain GCA_901343595v1
-        html chainNet
 
     track chainNetGCA_901343595v1Viewnet
     shortLabel Net
     view net
     visibility dense
     parent chainNetGCA_901343595v1
 
         track netGCA_901343595v1_MONAX5
         parent chainNetGCA_901343595v1Viewnet
         subGroups view=net
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5
-        html chainNet
 
 ##############################################################################
 # GCF_003668045.3 - Chinese hamster - Cricetulus griseus - taxId: 10029 - mammal
 ##############################################################################
 track chainNetGCF_003668045.3
 compositeTrack on
 shortLabel Chinese hamster Chain/Net
 longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -174,48 +174,47 @@
     track chainNetGCF_003668045.3Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCF_003668045.3
     spectrum on
 
         track chainGCF_003668045.3
         parent chainNetGCF_003668045.3Viewchain
         subGroups view=chain
         shortLabel Chinese hamster Chain
         longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) Chained Alignments
         type bigChain GCF_003668045.3
         bigDataUrl /gbdb/$D/bbi/chainNet/chainGCF_003668045.3.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_003668045.3Link.bb
-        html chainNet
 
     track mafNetGCF_003668045.3Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_003668045.3
 
         track netGCF_003668045.3
         parent mafNetGCF_003668045.3Viewnet
         subGroups view=net
         shortLabel Chinese hamster mafNet
         longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_003668045.3.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_003668045.3.net.summary.bb
         speciesOrder GCF_003668045.3
-        html chainNet
+        speciesLabels GCF_003668045.3="Chinese hamster"
 
 ##############################################################################
 # GCF_009829145.1 - lance-tailed manakin - Chiroxiphia lanceolata - taxId: 296741 - birds
 ##############################################################################
 track chainNetGCF_009829145.1
 compositeTrack on
 shortLabel lance-tailed manakin Chain/Net
 longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -232,48 +231,47 @@
     track chainNetGCF_009829145.1Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCF_009829145.1
     spectrum on
 
         track chainGCF_009829145.1
         parent chainNetGCF_009829145.1Viewchain
         subGroups view=chain
         shortLabel lance-tailed manakin Chain
         longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) Chained Alignments
         type bigChain GCF_009829145.1
         bigDataUrl /gbdb/$D/bbi/chainNet/chainGCF_009829145.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_009829145.1Link.bb
-        html chainNet
 
     track mafNetGCF_009829145.1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_009829145.1
 
         track netGCF_009829145.1
         parent mafNetGCF_009829145.1Viewnet
         subGroups view=net
         shortLabel lance-tailed manakin mafNet
         longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_009829145.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_009829145.1.net.summary.bb
         speciesOrder GCF_009829145.1
-        html chainNet
+        speciesLabels GCF_009829145.1="lance-tailed manakin"
 
 ##############################################################################
 # GCF_002742125.1 - Rambouillet sheep - Ovis aries - taxId: 9940 - mammal
 ##############################################################################
 track chainNetGCF_002742125.1
 compositeTrack on
 shortLabel Rambouillet sheep Chain/Net
 longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -324,51 +322,53 @@
     track mafNetGCF_002742125.1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_002742125.1
 
         track netGCF_002742125.1
         parent mafNetGCF_002742125.1Viewnet
         subGroups view=net
         shortLabel Rambouillet sheep mafNet
         longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.summary.bb
         speciesOrder GCF_002742125.1
-        html chainNet
+        speciesLabels GCF_002742125.1="Rambouillet sheep"
 
         track synNetGCF_002742125.1
         parent mafNetGCF_002742125.1Viewnet
         subGroups view=net
         shortLabel Rambouillet sheep mafNet
         longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.summary.bb
         speciesOrder GCF_002742125.1
+        speciesLabels GCF_002742125.1="Rambouillet sheep"
 
         track rbestNetGCF_002742125.1
         parent mafNetGCF_002742125.1Viewnet
         subGroups view=net
         shortLabel Rambouillet sheep mafNet
         longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.summary.bb
         speciesOrder GCF_002742125.1
+        speciesLabels GCF_002742125.1="Rambouillet sheep"
 
 ##############################################################################
 # GCA_018400075.1 - Zebrafish T5D - Danio rerio - taxId: 7955 - fish
 ##############################################################################
 track chainNetGCA_018400075.1
 compositeTrack on
 shortLabel Zebrafish T5D Chain/Net
 longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -385,48 +385,47 @@
     track chainNetGCA_018400075.1Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCA_018400075.1
     spectrum on
 
         track chainGCA_018400075.1
         parent chainNetGCA_018400075.1Viewchain
         subGroups view=chain
         shortLabel Zebrafish T5D Chain
         longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1) Chained Alignments
         type bigChain GCA_018400075.1
         bigDataUrl /gbdb/$D/bbi/chainNet/chainGCA_018400075.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/chainGCA_018400075.1Link.bb
-        html chainNet
 
     track mafNetGCA_018400075.1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCA_018400075.1
 
         track netGCA_018400075.1
         parent mafNetGCA_018400075.1Viewnet
         subGroups view=net
         shortLabel Zebrafish T5D mafNet
         longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_018400075.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_018400075.1.net.summary.bb
         speciesOrder GCA_018400075.1
-        html chainNet
+        speciesLabels GCA_018400075.1="Zebrafish T5D"
 
 ##############################################################################
 # GCF_016699485.2 - chicken (matMap) - Gallus gallus - taxId: 9031 - birds
 ##############################################################################
 track chainNetGCF_016699485.2
 compositeTrack on
 shortLabel Chicken Chain/Net
 longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -477,50 +476,53 @@
     track mafNetGCF_016699485.2Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_016699485.2
 
         track netGCF_016699485.2
         parent mafNetGCF_016699485.2Viewnet
         subGroups view=net
         shortLabel Chicken net
         longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.net.summary.bb
         speciesOrder GCF_016699485.2
+        speciesLabels GCF_016699485.2="Chicken/GRCg7b"
 
         track synNetGCF_016699485.2
         parent mafNetGCF_016699485.2Viewnet
         subGroups view=net
         shortLabel Chicken synNet
         longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.synNet.summary.bb
         speciesOrder GCF_016699485.2
+        speciesLabels GCF_016699485.2="Chicken/GRCg7b"
 
         track rbestNetGCF_016699485.2
         parent mafNetGCF_016699485.2Viewnet
         subGroups view=net
         shortLabel Chicken rbestNet
         longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.rbestNet.summary.bb
         speciesOrder GCF_016699485.2
+        speciesLabels GCF_016699485.2="Chicken/GRCg7b"
 
 ##############################################################################
 # GCF_000349665.1 - golden hamster - Gallus gallus - taxId: 9031 - birds
 ##############################################################################
 track chainNetGCF_000349665.1
 compositeTrack on
 shortLabel Golden hamster Chain/Net
 longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
@@ -571,35 +573,137 @@
     track mafNetGCF_000349665.1iewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_000349665.1
 
         track netGCF_000349665.1
         parent mafNetGCF_000349665.1iewnet
         subGroups view=net
         shortLabel Golden hamster net
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.summary.bb
         speciesOrder GCF_000349665.1
+        speciesLabels GCF_000349665.1="Golden hamster"
 
         track synNetGCF_000349665.1
         parent mafNetGCF_000349665.1iewnet
         subGroups view=net
         shortLabel Golden hamster synNet
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.synNet.summary.bb
         speciesOrder GCF_000349665.1
+        speciesLabels GCF_000349665.1="Golden hamster"
 
         track rbestNetGCF_000349665.1
         parent mafNetGCF_000349665.1iewnet
         subGroups view=net
         shortLabel Golden hamster rbestNet
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.summary.bb
         speciesOrder GCF_000349665.1
+        speciesLabels GCF_000349665.1="Golden hamster"
+
+##############################################################################
+# GCF_024166365.1 - Asiatic elephant - Elephas maximus indicus - taxId: 99487 - mammal
+##############################################################################
+track chainNetGCF_024166365.1
+compositeTrack on
+shortLabel Asiatic elephant Chain/Net
+longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+group compGeno
+noInherit on
+priority 100.1
+color 0,0,0
+altColor 100,50,0
+type bed 3
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+chainMinScore 3000
+chainLinearGap medium
+matrixHeader A, C, G, T
+otherDb GCF_024166365.1
+html chainNet
+
+    track chainNetGCF_024166365.1Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetGCF_024166365.1
+    spectrum on
+
+        track chainGCF_024166365.1
+        parent chainNetGCF_024166365.1Viewchain
+        subGroups view=chain
+        shortLabel Asiatic elephant Chain
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Chained Alignments
+        type bigChain GCF_024166365.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1Link.bb
+
+        track chainSynGCF_024166365.1
+        parent chainNetGCF_024166365.1Viewchain
+        subGroups view=chain
+        shortLabel Asiatic elephant Chain
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Syntenic Chained Alignments
+        type bigChain GCF_024166365.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1Link.bb
+
+        track chainRBestGCF_024166365.1
+        parent chainNetGCF_024166365.1Viewchain
+        subGroups view=chain
+        shortLabel Asiatic elephant Chain
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Reciprocal Best Chained Alignments
+        type bigChain GCF_024166365.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1Link.bb
+
+    track mafNetGCF_024166365.1Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetGCF_024166365.1
+
+        track netGCF_024166365.1
+        parent mafNetGCF_024166365.1Viewnet
+        subGroups view=net
+        shortLabel Asiatic elephant mafNet
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) mafNet Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.summary.bb
+        speciesOrder GCF_024166365.1
+        speciesLabels GCF_024166365.1="Asiatic elephant"
+
+        track synNetGCF_024166365.1
+        parent mafNetGCF_024166365.1Viewnet
+        subGroups view=net
+        shortLabel Asiatic elephant mafNet
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Syntenic Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.summary.bb
+        speciesOrder GCF_024166365.1
+        speciesLabels GCF_024166365.1="Asiatic elephant"
+
+        track rbestNetGCF_024166365.1
+        parent mafNetGCF_024166365.1Viewnet
+        subGroups view=net
+        shortLabel Asiatic elephant mafNet
+        longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) Reciprocal Best Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.summary.bb
+        speciesOrder GCF_024166365.1
+        speciesLabels GCF_024166365.1="Asiatic elephant"
+
+##############################################################################