10f674a1e8b0c153171383ed2e211c001fd36dec
braney
  Mon Jun 14 20:19:23 2021 -0700
add the creation of the cartVersion pseudo track to the beta trackDb
build #27517

diff --git src/hg/makeDb/trackDb/makefile src/hg/makeDb/trackDb/makefile
index 1d013a5..8a9ca07 100644
--- src/hg/makeDb/trackDb/makefile
+++ src/hg/makeDb/trackDb/makefile
@@ -1,331 +1,331 @@
 kentSrc = ../../..
 # Make your private trackDb with 
 #	make update
 # Your private trackDb with additional options, for example:
 #       make EXTRA="-strict -settings" update
 # Make it for genome-test with
 #	make alpha
 # Make for ENCODE reporting (includes release alpha and release beta)
 #	make encodeReport
 
 # DO NOT RUN MULTIPLE INSTANCES OF THIS SCRIPT 
 # Because it creates temporary files in the current directory 
 # before loading them into the database.
 
 # Browser supports multiple trackDb's so that individual developers
 # can change things rapidly without stepping on other people's toes. 
 # Usually when updating it is best to update your own trackDb and
 # test it to make sure it works and that you have git updated all
 # of trackDb/ before doing a make alpha. Note that you
 # must specify which trackDb you are using in your .hg.conf file
 # or in the cgi-bin-$(USER)/hg.conf file. Something like: 
 # db.trackDb=trackDb_YourUserName
 
 # note:  new group ARCHIVED_DBS created for assemblies still needed
 # to support Conservation tracks in other assemblies.  These should
 # have only chromInfo table on hgwbeta and RR.  make will not rebuild
 # trackDb on hgwdev unless the db is specified explicitly on the 
 # command line.
 
 include ../../../inc/common.mk
 
 DBS = \
 	ailMel1 \
 	allMis1 \
 	amaVit1 geoFor1 melUnd1 \
 	ambMex1 ambMex2 \
 	ancCey1 \
 	anoCar1 anoCar2 \
 	anoGam1 anoGam3 \
 	aotNan1 \
 	apiMel1 \
 	apiMel2	\
 	aplCal1 \
 	aptMan1 \
 	aquChr2 \
 	ascSuu1 \
 	balAcu1 \
 	bisBis1 \
 	bosTau2 bosTau3 bosTau4 bosTau5 bosTau6 bosTau7 bosTau8 bosTau9 \
 	braFlo1 braFlo2 \
 	bruMal1 bruMal2 \
 	burXyl1 \
 	caeAng1 caeAng2 \
 	caeJap1 caeJap2 caeJap3 caeJap4 \
 	caePb1 caePb2 caePb3 \
 	caeRem1 caeRem2 caeRem3 caeRem4 \
 	caeSp111 \
 	caeSp51 \
 	caeSp71 \
 	caeSp91 \
 	calJac1 calJac3 calJac4 \
 	calMil1 \
 	canFam1 canFam2 canFamPoodle1 canFam3 canFam4 canFam5 canFam6 \
 	casCan1 \
 	cavApe1 cavPor3 \
 	cb1 cb2 cb3 cb4 \
 	ce2 ce3 ce4 ce5 ce6 ce7 ce8 ce9 ce10 ce11 \
 	cebCap1 \
 	centromeres1 \
 	cerAty1 \
 	cerSim1 \
 	chiLan1o \
 	chlSab2 \
 	choHof1 \
 	chrPic1 chrPic2 \
 	ci1 ci2 ci3 cioSav2 \
 	cioSav1 \
 	colAng1 \
 	cotJap2 \
 	criGri1 criGriChoV1 criGriChoV2 \
 	danRer3 danRer4 danRer5 danRer6 danRer7 danRer10 danRer11 \
 	dasNov1 dasNov2 dasNov3 \
 	dipOrd1 dipOrd2 \
 	dirImm1 \
 	dm1 dm2 dm3 dm6 \
 	dp2 dp3 \
 	droAna1 droAna2 \
 	droEre1 \
 	droGri1 \
 	droMoj1 droMoj2 \
 	droPer1 \
 	droSec1 \
 	droSim1 droSim2 \
 	droVir1 droVir2 droVir3 \
 	droYak1 droYak2 \
 	eboVir3 eboVir2 eboVir1 bunEbo1 sudEbo1 resEbo1 taiEbo1 zaiEbo1 \
 	echTel1 echTel2 \
 	enhLutNer1 \
 	equCab1 equCab2 equCab3 \
 	eriEur1 eriEur2 \
 	eulFla1 \
 	eulMac1 \
 	falciparum \
 	felCat3 felCat4 felCat5 felCat8 felCat9 \
 	ficAlb1 \
 	fr1 fr2 fr3 \
 	fukDam1 \
 	gadMor1 \
 	galGal2 galGal3 galGal4 galGal5 galGal6 \
 	galVar1 \
 	gasAcu1 \
 	gorGor1 gorGor2 gorGor3 gorGor4 gorGor5 gorGor6 \
 	h1n1 \
 	haeCon1 haeCon2 \
 	hetBac1 \
 	hetGla1 hetGla2 \
 	hg16 hg17 hg18 hg19 hg38 hg19Haps hg19Patch2 hg19Patch5 hg19Patch9 hg19Patch10 hg38Patch7 hg38Patch9 hg38Patch11 \
 	latCha1 \
 	loaLoa1 \
 	loxAfr1 loxAfr2 loxAfr3 \
 	macEug1 macEug2 \
 	macFas5 \
 	macNem1 \
 	manLeu1 \
 	manPen1 \
 	marVir1 \
 	melGal1 melGal5 \
 	melHap1 \
 	melInc1 melInc2 \
 	micMur1 micMur2 micMur3 \
 	micOch1 \
 	mm6 mm7 mm8 mm9 mm10 mm10Patch1 mm10Strains1 mm10Patch4 GRCm38B mm39 \
 	monDom1 monDom4 monDom5 \
 	musFur1 \
 	myoLuc1 myoLuc2 \
 	nanPar1 \
 	nasLar1 \
 	necAme1 \
 	nemVec1 \
 	neoSch1 \
 	nomLeu1 nomLeu2 nomLeu3 \
 	ochPri2 ochPri3 \
 	oncVol1 \
 	orcOrc1 \
 	oreNil1 oreNil2 oreNil3 \
 	ornAna1 ornAna2 \
 	oryCun1 oryCun2 \
 	oryLat1 oryLat2 \
 	otoGar1 otoGar3 \
 	oviAri1 oviAri3 oviAri4 \
 	oxyTri2 \
 	panPan1 panPan2 panPan3 \
 	panRed1 \
 	panTro1 panTro2 panTro3 panTro4 panTro5 panTro6 \
 	papHam1 papAnu2 papAnu3 papAnu4 \
 	perManBai1 \
 	petMar1 petMar2 petMar3 \
 	plasFalc3D7V12 \
 	poeRet1 \
 	ponAbe2 ponAbe3 \
 	priExs1 \
 	priPac1 priPac2 priPac3 \
 	proCap1 \
 	proCoq1 \
 	pteVam1 tarSyr1 tarSyr2 \
 	repeats2 \
 	rheMac2 rheMac3 rheMac7 rheMac8 rheMac10 \
 	rhiBie1 \
 	rhiRox1 \
 	rn3 rn4 rn5 rn6 rn7 \
 	rouAeg1 \
 	sacCer1 sacCer2 sacCer3 \
 	saiBol1 \
 	sarHar1 \
 	sc1 \
 	sorAra1 sorAra2 \
 	speTri1 speTri2 \
 	strPur1 strPur2 strPur4 \
 	strRat1 strRat2 \
 	susScr1 susScr2 susScr3 susScr11 \
 	taeGut1 taeGut2 \
 	tetNig1 tetNig2 \
 	thaSir1 \
 	triCas2 \
 	triMan1 \
 	triSpi1 \
 	triSui1 \
 	tupBel1 \
 	tupChi1 \
 	turTru1 turTru2 \
 	venter1 \
 	vicPac1 vicPac2 \
 	wuhCor1 \
 	xenLae2 \
 	xenTro1 xenTro2 xenTro3 xenTro7 xenTro9 xenTro10
 
 ARCHIVED_DBS = \
 	rheMac1 \
 	danRer1 \
 	mm5 \
 	mm6 \
 	danRer2
 
 # if trix build breaks, disable by setting to /bin/true instead of ./buildTrix
 # BUILD_TRIX = /bin/true
 BUILD_TRIX = ./buildTrix
 HIVE_TRIX = /hive/data/inside/trix
 DATA_TRIX = /data/trix
 ALPHA_MACHINE = hgwdev.gi.ucsc.edu
 BETA_MACHINE = qateam@hgwbeta.soe.ucsc.edu
 PUBLIC_MACHINE = qateam@hgw0.soe.ucsc.edu
 
 # For the new demo-$USER machines, the "USER" passed in to makefile contains a hyphen which
 # needs to be replaced with an underscore for mysql table names.
 USERTABLE = $(shell echo ${USER} | sed -e 's/-/_/g')
 
 update: ${DBS:%=%_update}
 	${MKDIR} ${CGI_BIN}-${USER}/encode
 %_update:
 	./loadTracks -addVersion ${EXTRA} trackDb_${USERTABLE} hgFindSpec_${USERTABLE} $*
 	./checkMetaDb alpha metaDb_${USERTABLE} $*
 	# now build the relatedTracks table for each db
 	./buildRelatedTracks relatedTrack_${USERTABLE} $*
 	rm -rf /dev/shm/trackDbCache/$*.trackDb_${USERTABLE}
 
 #  if you want to test track search tool with your own trix file
 #	rm -f ${DBS:%=${HIVE_TRIX}/%_trackDb_${USERTABLE}.{ixx,ix}}
 #	HGDB_TRACKDB=trackDb_${USERTABLE} ${BUILD_TRIX} trackDb_${USERTABLE} metaDb_${USERTABLE} ${CGI_BIN}-${USER}/encode/cv.ra ${ALPHA_MACHINE} ${HIVE_TRIX} ${DBS}
 # you'll also need to set browser.trixPath to point to your trix file
 # see kent/src/product/ex.hg/conf for details
 
 alpha: clean
 	${GIT} pull
 	${MKDIR} ${CGI_BIN}/encode
 	${MAKE} alpha_all
 
 alpha_all: ${DBS:%=%_alpha}
 
 %_alpha:
 	./loadTracks -addVersion ${EXTRA} -release=alpha trackDb hgFindSpec $*
 	./checkMetaDb alpha metaDb $*
 	rm -f ${HIVE_TRIX}/$*_trackDb.{ixx,ix}}
 	HGDB_TRACKDB=trackDb ${BUILD_TRIX} trackDb metaDb cv/alpha/cv.ra ${ALPHA_MACHINE} ${HIVE_TRIX} $*
 	./makeTrixLinks trackDb ${HIVE_TRIX} $*
 	# now build the relatedTracks table for each db
 	./buildRelatedTracks relatedTrack $*
 	rm -rf /dev/shm/trackDbCache/$*.trackDb
 
 onbeta:	/cluster/home/${USER}/.hg.conf.beta
 
 betaTest: onbeta clean 
 	${MAKE} betaTest_all
 
 betaTest_all: ${DBS:%=%_betaTest}
 
 beta: onbeta clean 
 	${GIT} pull
 	${MAKE} beta_all
 
 beta_all: ${DBS:%=%_beta}
 
 %_betaTest:
 	# now do loads on hgwbeta
-	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks ${EXTRA} -strict -remoteLogin=${BETA_MACHINE} -release=beta trackDb_betaTest hgFindSpec_betaTest $*
+	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks -addVersion ${EXTRA} -strict -remoteLogin=${BETA_MACHINE} -release=beta trackDb_betaTest hgFindSpec_betaTest $*
 
 %_beta:
 	# now do loads on hgwbeta
 	-ssh  ${BETA_MACHINE} find /gbdb/$*  -type f -size +1c  > $*.gbdbList.txt
-	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks ${EXTRA} -strict -gbdbList=$*.gbdbList.txt -release=beta trackDb hgFindSpec $*
+	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks -addVersion ${EXTRA} -strict -gbdbList=$*.gbdbList.txt -release=beta trackDb hgFindSpec $*
 	rm  -f $*.gbdbList.txt
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./checkMetaDb beta metaDb $*
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta HGDB_TRACKDB=trackDb ${BUILD_TRIX} trackDb metaDb cv/beta/cv.ra ${BETA_MACHINE} ${DATA_TRIX} $*
 	# now make files for hgwdev-beta (we share the tables with hgwbeta)
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta HGDB_TRACKDB=trackDb ${BUILD_TRIX} trackDb metaDb cv/beta/cv.ra ${ALPHA_MACHINE} ${HIVE_TRIX} $*
 	# now build the relatedTracks table for each db
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./buildRelatedTracks relatedTrack $*
 	-ssh  ${BETA_MACHINE} rm -rf /dev/shm/trackDbCache/$*.trackDb
 
 publicTest: onbeta clean
 	${MAKE} publicTest_all
 
 publicTest_all: ${DBS:%=%_publicTest}
 
 public: onbeta clean
 	${GIT} pull
 	${MAKE} public_all
 
 public_all: ${DBS:%=%_public}
 
 %_publicTest:
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks ${EXTRA} -strict -remoteLogin=${PUBLIC_MACHINE} -release=public trackDb_publicTest hgFindSpecTest_publicTest $*
 
 %_public:
 	-ssh  ${PUBLIC_MACHINE} find /gbdb/$*  -type f -size +1c  > $*.gbdbList.txt
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./loadTracks ${EXTRA} -strict -gbdbList=$*.gbdbList.txt -release=public trackDb_public hgFindSpec_public $*
 	rm -f $*.gbdbList.txt
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./checkMetaDb public metaDb_public $*
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta HGDB_TRACKDB=trackDb_public ${BUILD_TRIX} trackDb_public metaDb_public cv/public/cv.ra ${BETA_MACHINE} ${DATA_TRIX} $*
 	# now build the relatedTracks table for each db
 	HGDB_CONF=/cluster/home/${USER}/.hg.conf.beta ./buildRelatedTracks relatedTrack $*
 	-ssh  ${BETA_MACHINE} rm -rf /dev/shm/trackDbCache/$*.trackDb_public
 
 # this will fail if we are not in a beta checkout:
 checkbeta:
 	${GIT} branch | egrep '^[*] v[0-9]+_branch' > /dev/null
 
 # not sure if anyone actually uses the target below. It used to be "beta".
 buildBeta: checkbeta clean strict
 
 encodeReport:
 	${GIT} pull
 	./loadTracks ${EXTRA} trackDb_encodeReport hgFindSpec ${DBS}
 
 listDbs:
 	@echo "# databases listed in trackDb/makefile DBS variable, with table counts"
 	@for D in ${DBS}; do \
 	    C=`hgsql -N -e "show tables;" $${D} 2> /dev/null | wc -l`; \
 	    if [ "$${C}" -gt 0 ]; then \
 		echo -e "$${D}\t$${C}"; \
 	    fi \
 	done
 
 test:
 	tdbQuery -check -release=alpha -strict "select count(*) from *" >/dev/null
 	tdbQuery -check -release=beta -strict "select count(*) from *" >/dev/null
 	tdbQuery -check -release=public -strict "select count(*) from *" >/dev/null
 
 # Get rid of symbolic links (created by lower-level makefiles):
 clean:
 	find . -type l -exec rm {} \;