4492d656288371cb1802c3a38217acb11bde6368
markd
  Thu Jun 15 11:45:05 2023 -0700
removed obsolete attempt to integrate CHM13 with GenArk

diff --git src/hg/makeDb/doc/chm13v2.0userData/makefile src/hg/makeDb/doc/chm13v2.0userData/makefile
deleted file mode 100644
index fd82601..0000000
--- src/hg/makeDb/doc/chm13v2.0userData/makefile
+++ /dev/null
@@ -1,80 +0,0 @@
-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
-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 microsatellites \
-         sgdpCopyNumber encode t2tRepeatMasker
-
-# 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 catLiftOffGenesV1.rna.fa.gz catLiftOffGenesV1.protein.fa.gz
-
-.SECONDARY:
-MAKEFLAGS += --check-symlink-times
-
-#  not hubCheck -checkSettings currently has false positives, so not using
-all: ${userTrackDbFile} bbiInstall htmlInstall liftOverInstall geneInstall
-	hubCheck ${stageUrl}
-
-# ensure spaces separate the stanzas
-${userTrackDbFile}: ${tracks:%=trackDb/%.trackDb.txt}
-	awk 'FNR==1{print ""} {print $$0}'  $^ > $@
-
-# make bbi links for directories
-.PHONY: bbiInstall bbiInstall_%
-bbiInstall: ${tracks:%=${bbiBuildDir}/${asmId}.%}
-
-# create symlink if it doesn't exist
-${bbiBuildDir}/${asmId}.%:
-	ln -sf ../trackData/$* ${bbiBuildDir}/${asmId}.$*
-
-# copy HTML to build and link to the stage dir
-.PHONY: htmlInstall
-htmlInstall: ${tracksWithHtml:%=${htmlStageDir}/${asmId}.%.html}
-
-${htmlStageDir}/${asmId}.%.html: html/%.html
-	@mkdir -p $(dir $@)
-	cp -f $< $@
-
-${htmlStageDir}/%.png: html/%.png
-	@mkdir -p $(dir $@)
-	cp -f $< $@
-
-# install liftOver files
-liftOverInstall: ${hgLiftOverFiles:%=${liftOverStageDir}/%}
-
-${liftOverStageDir}/%: ${liftOverDataDir}/%
-	@mkdir -p $(dir $@)
-	ln -sf $< $@
-
-# install gene downloads
-geneInstall: ${catGxfFiles:%=${geneStageDir}/%}
-
-${geneStageDir}/%: ${geneDataDir}/%
-	@mkdir -p $(dir $@)
-	ln -sf $$(realpath --relative-to=${geneStageDir} $<) $@
-
-
-clean:
-	rm -f ${userTrackDbFile}