8cbdb800a1d6e5a699372b44567f77ef6ff4cc37
hiram
  Thu Apr 21 12:21:36 2022 -0700
adding NCBI RefSeq genes refs #29278

diff --git src/hg/makeDb/doc/chm13v2.0/makefile src/hg/makeDb/doc/chm13v2.0/makefile
index 43e20b9..7f880ae 100644
--- src/hg/makeDb/doc/chm13v2.0/makefile
+++ src/hg/makeDb/doc/chm13v2.0/makefile
@@ -1,86 +1,87 @@
 
 accession = GCA_009914755.4
 asmId = ${accession}_T2T-CHM13v2.0
 stageDir = /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/${asmId}
 pushFromDir = /hive/data/genomes/asmHubs//GCA/009/914/755/${accession}
 pushToDir = /mirrordata/hubs/GCA/009/914/755/${accession}
 
 # default set of hub track html description files
 
 htmlFiles = html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.description.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html \
+html/GCA_009914755.4_T2T-CHM13v2.0.refSeqComposite.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html
 
 # tracks not used
 
 notPushed = html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html
 
 # files used to construct a useOneFile hub.txt
 hubTxt = hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt \
 hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt \
 trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt
 
 alpha:: singleFileHub
 	@printf "# setting up hub files for hgdownload-test staging\n"
 	make stageFiles
 	make test
 
 stageFiles: $(htmlFiles:%=%stageFiles)
 %stageFiles:
 	@rm -f "${stageDir}/$*"
 	@cp --remove-destination -p "$*" "${stageDir}/$*"
 
 # verify the hub is functioning OK on hgwdev/genome-test from hgdownload-test
 test:
 	@printf "# verify hub is functioning from hgdownload-test.gi.ucsc.edu\n"
 	hubCheck -checkSettings "https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
 	@printf "hubCheck OK\n"
 	@printf "track count: %d tracks via API list tracks\n" "`curl -L "https://genome-test.gi.ucsc.edu/list/tracks?genome=GCA_009914755.4;trackLeavesOnly=1;hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"  2> /dev/null | python -mjson.tool | egrep ": {$$"  | tr -d '"' | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w`"
 	@printf "should be more than 70 tracks\n"
 
 
 # verify the hub is functioning OK from hgdownload.soe.ucsc.edu
 verify:
 	@printf "# verify hub is functioning from hgdownload.soe.ucsc.edu\n"
 	hubCheck "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
 	@printf "hubCheck OK\n"
 	@printf "track count: %d tracks via API list tracks\n" "`curl -L "https://apibeta.soe.ucsc.edu/list/tracks?genome=GCA_009914755.4;trackLeavesOnly=1;hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"  2> /dev/null | python -mjson.tool | egrep ": {$$"  | tr -d '"' | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w`"
 	@printf "should be more than 70 tracks\n"
 
 # user must have login permissions as qateam to hgdownload
 verifyLogin:
 	@printf "# verify login to qateam@hgdownload functions, should see the date\n"
 	@ssh qateam@hgdownload.soe.ucsc.edu date 2>&1 | grep -v "X11 forwarding"
 	@printf "# login to qateam@hgdownload OK\n"
 
 # push the hub to hgdownload
 public: verifyLogin
 	@printf "pushing to hgdownload\n" 1>&2
 	rsync --exclude="hub.txt" --exclude="download.hub.txt" --stats -a -L -P "${pushFromDir}/" "qateam@hgdownload.soe.ucsc.edu:${pushToDir}/" 2>&1 | grep -v "X11 forwarding request" || true
 	rsync --stats -a -L -P "${pushFromDir}/download.hub.txt" "qateam@hgdownload.soe.ucsc.edu:${pushToDir}/hub.txt" 2>&1 | grep -v "X11 forwarding request" || true
 	@printf "# successful rsync\n" 1>&2
 	make verify
 
 clean::
 	rm -f hub.txt
 
 singleFileHub: ${hubTxt}
 	@rm -f hub.txt
 	@grep -v genomesFile hub/${asmId}.hub.txt > hub.txt
 	@printf "useOneFile on\n\n" >> hub.txt
 	@grep -v trackDb hub/${asmId}.genomes.txt >> hub.txt
 	@echo >> hub.txt
 	@cat trackDb/${asmId}.trackDb.txt >> hub.txt
 	@cp --remove-destination -p hub.txt ${stageDir}/${asmId}.singleFile.hub.txt
 	@cp --remove-destination -p hub.txt ${stageDir}/${asmId}.download.hub.txt
 	@cp --remove-destination -p hub/${asmId}.groups.txt ${stageDir}/
 	@cp --remove-destination -p hub/${asmId}.genomes.txt ${stageDir}/
 	cp --remove-destination -p hub/${asmId}.hub.txt ${stageDir}/
 	@rm -f hub.txt