6e38471f9e03b95d1a26a10a4e71616b7f2e6837
markd
  Mon Apr 11 17:31:15 2022 -0700
renamed ulgy chr13 directory to keep Hiram sane

diff --git src/hg/makeDb/doc/chm13v2.0userData/makefile src/hg/makeDb/doc/chm13v2.0userData/makefile
new file mode 100644
index 0000000..990c118
--- /dev/null
+++ src/hg/makeDb/doc/chm13v2.0userData/makefile
@@ -0,0 +1,80 @@
+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
+
+.SECONDARY:
+MAKEFLAGS += --check-symlink-times
+
+all: ${userTrackDbFile} bbiInstall htmlInstall liftOverInstall geneInstall
+	cd ${asmBuildDir} && ./doTrackDb.bash
+	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}