785f5d95987a916b8c37021dfa2e7ec0271fff34
kent
  Wed May 21 16:17:11 2014 -0700
Making it so that the ENCODE data warehouse doesn't even try to compile under Mac OS.  It doesn't need to, and Mac OS lacks some of the libraries it uses.
diff --git src/hg/makefile src/hg/makefile
index 855944a..5a626dd 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -1,298 +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 hgLogin hgPcr hgSession hgSuggest \
         hgTables hgTracks hgTrackUi hgUserSuggestion hgc hgApi cartDump near/hgNear \
 	hgLiftOver hgVai visiGene/hgVisiGene \
 	encode/hgEncodeDataVersions \
 	encode/hgEncodeVocab encode/hgEncodeApi \
 	phyloGif hgCustom hgPal hgFileUi hgFileSearch\
 	makeDb/hgCgiData js htdocs/style hgMirror
 
 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 \
             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
+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 \
 	gigAssembler/checkAgpAndFa \
 	hgsql \
 	hgsqldump \
 	maskOutFa \
 	mrnaToGene \
 	ratStuff/mafsInRegion \
 	ratStuff/mafSpeciesSubset \
 	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 \
-#	encode3 \
+	${buildRefresh} \
 	fakeFinContigs \
 	fakeOut \
 	ffaToFa \
 	fishClones \
 	fqToQa \
 	fqToQac \
 	fragPart \
 	gbGetEntries \
 	gbOneAcc \
 	gbToFaRa \
 	geneBounds \
 	getFeatDna \
 	getRna \
 	getRnaPred \
 	gpStats \
 	gpToGtf \
 	gpcrParser \
 	gsBig \
 	hgTablesTest \
 	hgChroms \
 	hgGetAnn \
 	hgKnownGeneList \
 	hgSelect \
 	hgSpeciesRna \
 	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