ab44b461105c3ef94aaa361e148ed6e9a943ad08
markd
  Sun Apr 17 17:59:20 2022 -0700
fixed color table in sedefSegDups HTML

diff --git src/hg/makeDb/doc/chm13v2.0userData/makefile src/hg/makeDb/doc/chm13v2.0userData/makefile
index e5d2661..bb1555f 100644
--- src/hg/makeDb/doc/chm13v2.0userData/makefile
+++ src/hg/makeDb/doc/chm13v2.0userData/makefile
@@ -1,25 +1,24 @@
 SHELL = /bin/bash
 
 ncbiAcc = GCA_009914755.4
 asmName= T2T-CHM13v2.0
 asmId = ${ncbiAcc}_${asmName}
 asmBuildDir = /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/${asmId}
 asmStageDir = /hive/data/genomes/asmHubs/GCA/009/914/755/${ncbiAcc}
 trackDataDir = ${asmBuildDir}/trackData
 bbiBuildDir = ${asmBuildDir}/bbi
-htmlBuildDir = ${asmBuildDir}/html
 htmlStageDir = ${asmStageDir}/html
 liftOverDataDir = ${asmBuildDir}/liftOver
 liftOverStageDir = ${asmStageDir}/liftOver
 geneDataDir = ${trackDataDir}/catLiftOffGenesV1
 geneStageDir = ${asmStageDir}/genes
 
 stageUrl = https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt
 
 userTrackDbFile = ${asmBuildDir}/${asmId}.userTrackDb.txt
 
 tracks = proseq rnaseq cytoBandMapped sedefSegDups rdnaModel catLiftOffGenesV1 hgLiftOver \
          censat hgUnique clinVar20220313 gwasSNPs2022-03-08 dbSNP155
 
 # snakes needs chromAlias fix:
 # hgCactus
@@ -40,35 +39,31 @@
 ${userTrackDbFile}: ${tracks:%=trackDb/%.trackDb.txt}
 	awk 'FNR==1{print ""} {print $$0}'  $^ > $@
 
 # make bbi links for directories
 .PHONY: bbiInstall bbiInstall_%
 bbiInstall: ${tracks:%=${bbiBuildDir}/${asmId}.%}
 
 # create symlink if it doesn't exist
 ${bbiBuildDir}/${asmId}.%:
 	ln -sf ../trackData/$* ${bbiBuildDir}/${asmId}.$*
 
 # copy HTML to build and link to the stage dir
 .PHONY: htmlInstall
 htmlInstall: ${tracksWithHtml:%=${htmlStageDir}/${asmId}.%.html}
 
-${htmlStageDir}/${asmId}.%.html: ${htmlBuildDir}/${asmId}.%.html
-	@mkdir -p $(dir $@)
-	ln -sf $< $@
-
-${htmlBuildDir}/${asmId}.%.html: html/%.html
+${htmlStageDir}/${asmId}.%.html: html/%.html
 	@mkdir -p $(dir $@)
 	cp -f $< $@
 
 # install liftOver files
 liftOverInstall: ${hgLiftOverFiles:%=${liftOverStageDir}/%}
 
 ${liftOverStageDir}/%: ${liftOverDataDir}/%
 	@mkdir -p $(dir $@)
 	ln -sf $< $@
 
 # install gene downloads
 geneInstall: ${catGxfFiles:%=${geneStageDir}/%}
 
 ${geneStageDir}/%: ${geneDataDir}/%
 	@mkdir -p $(dir $@)