0ac694cd00be11bb7ccf3a678e3d8af7fecce04b
galt
  Wed Aug 12 12:16:05 2015 -0700
Cleaning up by removing hgsqlLocal and hgsqldumpLocal and references to them. These are obsolete both because Jing says they are not used by Cancer browser anymore, not does our documentation refer to it, nor do the makefiles and scripts actually work anymore, and finally because hgsql now has -profile=localDb option.  Jing says it is OK to nuke this old junk. Of course it will live in history as it should.

diff --git src/hg/makefile src/hg/makefile
index 5ec9dce..a7c1339 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -1,307 +1,305 @@
 # Build all directories in utils
 
 kentSrc = ..
 include ${kentSrc}/inc/localEnvironment.mk
 
 # 	$Id: makefile,v 1.156 2010/03/03 02:53:30 markd Exp $
 
 BROWSER_BINS=cartReset das hgBlat makeDb/hgCgiData hgConvert hgHubConnect \
         hgGateway hgGene hgGenome hgIntegrator hgLogin hgPcr hgSession hgSuggest \
         hgTables hgTracks hgTrackUi hgUserSuggestion hgc hgApi cartDump near/hgNear \
 	hgLiftOver hgVai visiGene/hgVisiGene hgMenubar \
 	encode/hgEncodeDataVersions \
 	encode/hgEncodeVocab encode/hgEncodeApi \
 	phyloGif hgCustom hgPal hgFileUi hgFileSearch\
 	makeDb/hgCgiData js htdocs/style hgMirror hgBeacon
 
 ifdef LOWELAB
     BROWSER_BINS += $(HOME)/lowelab/src/browser/tooltip $(HOME)/lowelab/src/browser/chooseorg
 endif
 
 BROWSER_LOADERS = makeDb/hgLoadBed makeDb/hgLoadWiggle makeDb/hgLoadMaf
 
 ifneq ($(findstring $(shell hostname),hgwdev hgwbeta),)
     ENCODE_FILES = encode3/encodeDataWarehouse
 endif
 
 
 TEST_DIRS = lib autoDtd autoSql blastToPsl checkTableCoords embossToPsl \
             genePredSingleCover genePredHisto genePredToBed genePredToGtf \
 	    genePredToMafFrames gbGetEntries hgGetAnn liftAcross liftOver \
             mouseStuff mrnaToGene pslCDnaFilter pslDiff pslHisto \
             pslPartition pslSelect pslStats pslSwap pslToBed spideyToPsl \
 	    sqlToXml xmlToSql utils
 
 BROKEN_TEST_DIRS = liftOver scaffoldFaToAgp
 
 BAD_DIRS = \
 	altGraph \
 	cgiExample \
 	geneOverlap \
 	hgBatch \
 	makeSeqs \
 	oneShot \
 	synMap \
 	encode \
 	wikiPlot
 
 # can not build this on Mac OSX - has functions not supported
 UNAME_S := $(shell uname -s) 
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=encode3
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	autoDtd \
 	autoSql \
 	autoXml \
 	bedSort \
 	liftUp \
 	liftOver \
 	bedIntersect \
 	bedItemOverlapCount \
 	bedToGenePred \
 	blastToPsl \
 	checkCoverageGaps \
 	checkHgFindSpec \
 	checkTableCoords \
 	dbTrash \
 	encode3/validateFiles \
 	encode3/validateManifest \
 	estOrient \
 	featureBits \
 	genePredHisto \
 	genePredSingleCover \
 	genePredToBed \
 	genePredToFakePsl \
 	genePredToMafFrames \
 	getRna \
 	getRnaPred \
 	gigAssembler/checkAgpAndFa \
 	hgSpeciesRna \
 	hgsql \
 	hgsqldump \
 	maskOutFa \
 	mrnaToGene \
 	ratStuff/mafsInRegion \
 	ratStuff/mafSpeciesSubset \
 	ratStuff/mafToSnpBed \
 	pslCDnaFilter \
 	genePredCheck \
 	genePredToGtf \
 	pslCat \
 	pslCheck \
 	pslDropOverlap \
 	pslFilter \
 	pslHisto \
 	pslPairs \
 	pslPartition \
 	pslPretty \
 	pslRecalcMatch \
 	pslReps \
 	pslSelect \
 	pslSort \
 	pslStats \
 	pslSwap \
 	pslToBed \
 	pslToChain \
 	pslxToFa \
 	qaToQac \
 	qacAgpLift \
 	qacToQa \
 	qacToWig \
 	sqlToXml \
 	trfBig \
 	xmlCat \
 	xmlToSql
 
 # List of directories to build at UCSC
 UTIL_DIRS = \
 	affyTransciptome \
 	agpCloneCheck \
 	agpCloneList \
 	agpAllToFaFile \
 	agpToFa \
 	agpToGl \
 	altSplice \
 	bedOrBlocks \
 	bedSplitOnChrom \
 	borfBig \
 	ctgFaToFa \
 	ctgToChromFa \
 	embossToPsl \
 	${buildRefresh} \
 	fakeFinContigs \
 	fakeOut \
 	ffaToFa \
 	fishClones \
 	fqToQa \
 	fqToQac \
 	fragPart \
 	gbGetEntries \
 	gbOneAcc \
 	gbToFaRa \
 	geneBounds \
 	getFeatDna \
 	gpStats \
 	gpToGtf \
 	gpcrParser \
 	gsBig \
 	hgTablesTest \
 	hgChroms \
 	hgGetAnn \
 	hgKnownGeneList \
 	hgSelect \
-	hgsqlLocal \
 	hgsqladmin \
-	hgsqldumpLocal \
 	hgsqlimport \
         hgsqlSwapTables \
         hgsqlTableDate \
 	intronEnds \
 	lib \
 	liftAcross \
 	liftAgp \
 	liftFrags \
 	lfsOverlap \
 	makeDb \
 	mdToNcbiLift \
 	mouseStuff \
 	near/hgCeOrfToGene \
 	near/hgClusterGenes \
 	near/hgEmblProtLinks \
 	near/hgExpDistance \
 	near/hgGoAssociation \
 	near/hgKnownToSuper \
 	near/hgMapToGene \
 	near/hgMapViaSwissProt \
 	near/hgProtIdToGenePred \
 	near/hgWormLinks \
 	near/pepPredToFa \
 	near/hgNearTest \
 	near/hgNetDist \
 	near/knownToHprd \
 	nci60 \
 	orthoMap \
 	patCount \
 	perf \
 	pslCoverage \
 	pslDiff \
 	pslFilterPrimers \
 	pslGlue \
 	pslHitPercent \
 	pslIntronsOnly \
 	pslQuickFilter \
 	pslSimp \
 	pslSortAcc \
 	pslSplitOnTarget \
 	pslUnpile \
 	qa \
 	ratStuff \
 	relPairs \
 	recycleDb \
 	reviewSanity \
 	rnaStructure \
 	sage \
 	scanRa \
 	semiNorm \
 	sim4big \
 	snpException \
 	snp \
 	spideyToPsl \
 	splitFa \
 	splitFaIntoContigs \
 	test \
 	txCds \
 	txGene \
 	txGraph \
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene
 
 APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
 
 all::    cgi utils
 
 hgLib:
 	cd lib && ${MAKE}
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 	cd altSplice/lib && $(MAKE)
 	cd altSplice/altSplice && $(MAKE) bedToExons
 	cd mouseStuff && $(MAKE) userApps
 	cd ratStuff && $(MAKE) userApps
 
 %.userApp: hgLib
 	cd $* && echo $* && $(MAKE)
 
 utils: $(APPS:%=%.utils)
 %.utils: hgLib
 	cd $* && echo $* && $(MAKE)
 
 # Compile only, the cgi's for those builds without write access
 #	to apache cgi-bin directories  (this compiles and links executables)
 
 compile: ${BROWSER_BINS:%=%.compile} ${BROWSER_LOADERS:%=%.compile}
 %.compile: hgLib
 	cd $* && echo $* && $(MAKE) compile
 
 # Build cgi's
 #   cgi: Destination for the binaries is /usr/local/apache/cgi-bin-${USER}
 
 cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
 %.bins: hgLib
 	cd $* && echo $* && $(MAKE)
 %.cgi: hgLib
 	cd $* && echo $* && $(MAKE) cgi
 
 #   alpha: Destination for the binaries is /usr/local/apache/cgi-bin/
 
 alpha:	 ${BROWSER_BINS:%=%.alpha} ${BROWSER_LOADERS:%=%.alpha} ${ENCODE_FILES:%=%.alpha}
 %.alpha: hgLib
 	cd $* && echo $* && $(MAKE) alpha
 
 #   beta: Destination for the binaries is /usr/local/apache/cgi-bin-beta/
 
 beta: ${BROWSER_BINS:%=%.beta} ${BROWSER_LOADERS:%=%.beta}
 %.beta: hgLib
 	cd $* && echo $* && $(MAKE) beta
 
 # install: Destination for the binaries is ${DESTDIR}/usr/local/apache/cgi-bin
 
 install: ${BROWSER_BINS:%=%.install} ${BROWSER_LOADERS:%=%.install}
 %.install: hgLib
 	cd $* && echo $* && $(MAKE) install
 
 clean::
 	cd lib && ${MAKE} clean
 	@for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 
 clean_utils::
 	@for D in ${UTIL_DIRS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 
 clean::	${TEST_DIRS:%=%.clean}
 
 %.clean:
 	cd $* && ${MAKE} clean
 
 testAll: $(APPS:%=%.testAll)
 
 %.testAll:
 	@test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true
 
 test::	${TEST_DIRS:%=%.test} testAll
 
 %.test: hgLib
 	cd $* && ${MAKE} test