190ba8082f1e7f99ab7ee3038b1b2eefb5791357
Merge parents 66e096c ed22a78
kate
  Thu Nov 10 17:26:32 2016 -0800
Resolving merge conflicts

diff --cc src/hg/makefile
index 22394e3,9551bf9..92d33bf
--- src/hg/makefile
+++ src/hg/makefile
@@@ -1,305 -1,305 +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 hgPublicSessions \
  	encode/hgEncodeDataVersions \
  	encode/hgEncodeVocab encode/hgEncodeApi \
- 	phyloGif hgCustom hgPal hgFileUi hgFileSearch\
+ 	phyloPng hgCustom hgPal hgFileUi hgFileSearch\
 -	makeDb/hgCgiData js htdocs/style hgMirror hgBeacon
 +	makeDb/hgCgiData js htdocs/style hgMirror hgBeacon hgGtexTrackSettings
  
  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 \
  	hgsqladmin \
  	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