5148aa7d55ecbad1137ae3cd4bb0c85b67e8fed3
markd
  Thu Apr 14 12:13:05 2022 -0700
added cat/liftoff rna and protein fastas

diff --git src/hg/makeDb/doc/chm13v2.0userData/makefile src/hg/makeDb/doc/chm13v2.0userData/makefile
index 582122f..f49914c 100644
--- src/hg/makeDb/doc/chm13v2.0userData/makefile
+++ src/hg/makeDb/doc/chm13v2.0userData/makefile
@@ -1,79 +1,79 @@
 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
 
 tracksWithHtml = $(filter-out cytoBandMapped,${tracks})
 
 hgLiftOverFiles = chm13v2-hg19.over.chain.gz chm13v2-hg38.over.chain.gz hg19-chm13v2.over.chain.gz hg38-chm13v2.over.chain.gz
 
-catGxfFiles = catLiftOffGenesV1.gff3.gz catLiftOffGenesV1.gtf.gz
+catGxfFiles = catLiftOffGenesV1.gff3.gz catLiftOffGenesV1.gtf.gz catLiftOffGenesV1.rna.fa.gz catLiftOffGenesV1.protein.fa.gz
 
 .SECONDARY:
 MAKEFLAGS += --check-symlink-times
 
 all: ${userTrackDbFile} bbiInstall htmlInstall liftOverInstall geneInstall
 	hubCheck ${stageUrl}
 
 # ensure spaces separate the stanzas
 ${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
 	@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 $@)
 	ln -sf $$(realpath --relative-to=${geneStageDir} $<) $@
 
 
 clean:
 	rm -f ${userTrackDbFile}