4abf44177745692dfda0cc4f93b2b20f2dd39ea2
kate
  Thu May 4 10:40:43 2017 -0700
Add tools for making barChart files (expMatrixToBarchartBed and bedJoinTabOffset) to user apps. Cleanup ws and provide for scripts in subdirs. refs #18736

diff --git src/utils/makefile src/utils/makefile
index 8ae92b8..d375456 100644
--- src/utils/makefile
+++ src/utils/makefile
@@ -1,244 +1,262 @@
 # Build all directories in utils
 
 kentSrc = ..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 # note: lists such as the following need to be defined *before*
 # they are used in the wildcard target rules.  An oddity of gnu make
 
 # define the list of user applications to build
 
 UTILS_APPLIST = \
 	addCols \
 	ave \
 	aveCols \
 	bamToPsl \
 	bedClip \
 	bedGraphToBigWig \
 	bedToBigBed \
 	bigBedInfo \
 	bigBedNamedItems \
 	bigBedSummary \
 	bigBedToBed \
 	bedCommonRegions \
 	bedGeneParts \
 	bedGraphPack \
 	bedPileUps \
 	bedRemoveOverlap \
 	bedRestrictToPositions \
 	bigWigAverageOverBed  \
 	bigWigCat \
 	bigWigCorrelate \
 	bigWigCluster \
 	bigWigInfo \
 	bigWigMerge \
 	bigWigSummary \
 	bigWigToBedGraph \
 	bigWigToWig \
 	calc \
 	catDir \
 	catUncomment \
 	chopFaLines \
 	colTransform \
 	countChars \
 	faAlign \
 	fastqToFa \
 	fastqStatsAndSubsample \
 	faCmp \
 	faCount \
 	faFilterN \
 	faFilter \
 	faFrag \
 	faNoise \
 	faOneRecord \
 	faPolyASizes \
 	faRandomize \
 	faRc \
 	faSize \
 	faSomeRecords \
 	faSplit \
 	faToFastq \
 	faToTab \
 	faToTwoBit \
 	faTrans \
 	findMotif \
 	headRest \
 	htmlCheck \
 	newProg \
 	newPythonProg \
 	nibFrag \
 	nibSize \
 	paraFetch \
 	paraSync \
 	pslLiftSubrangeBlat \
 	pslPosTarget \
 	pslScore \
 	pslToPslx \
 	randomLines \
 	raSqlQuery \
 	raToTab \
 	raToLines \
 	rmFaDups \
 	rowsToCols \
 	sizeof \
 	spacedToTab \
 	splitFile \
 	splitFileByColumn \
 	stringify \
 	subChar \
 	subColumn \
 	tabQuery \
 	tailLines \
 	textHistogram \
 	tickToDate \
 	timing \
 	toLower \
 	toUpper \
 	twoBitDup \
 	twoBitInfo \
 	twoBitToFa \
 	wigCorrelate \
 	wigToBigWig \
 	wordLine
 
 # list of utilities to build of interest only at UCSC
 
 UCSC_APPS = \
 	addCols \
 	aNotB \
 	aveCols \
 	ccCp \
 	convolve \
 	detab \
 	endsInLf \
 	faFlyBaseToUcsc \
 	faGapLocs \
 	faGapSizes \
 	faNcbiToUcsc \
 	faSimplify \
 	faToNib \
 	faTrimPolyA \
 	faTrimRead \
 	fixCr \
 	gapSplit \
 	gitTools \
 	gffPeek \
 	git-reports \
 	htmlPics \
 	jkUniq \
 	lineCount \
 	nt4Frag \
 	pslToXa \
 	scaffoldFaToAgp \
 	scrambleFa \
 	subs \
 	tableSum \
 	textHist2 \
 	udcCleanup \
 	undupFa \
 	upper \
 	venn \
 	verticalSplitSqlTable \
 	weedLines \
 	wigTestMaker
 
 # list of scripts to install
 
+USER_APP_SCRIPTS = \
+	bedJoinTabOffset \
+	expMatrixToBarchartBed
+
 SCRIPT_FILES = \
 	agpToLift \
 	apacheLogParse \
 	bedCollapse.pl \
 	bedFixBlockOverlaps \
 	bedOverlapMerge \
 	bedSingleCover.pl \
 	bedBetween \
 	doLocusName \
 	extToolsChromeParse \
 	iSync \
 	lodToBedScore \
 	matrixMerge \
 	mkMafFrames.pl \
 	patSeqFilterBulkAndAnnotate \
 	patSeqSummarizeDocs \
 	pslProtCnv \
 	pslSameGene \
 	tabRepl \
 	uniprotLift \
 	uniprotToTab \
-	bedJoinTabOffset \
-	expMatrixToBarchartBed \
 	ggTables \
 	ggGeneClasses \
 	ggGpmlToTag \
 	ggKgmlToTab \
 	ggMsrToTab \
 	ggPidToTab \
 	ggPpiToTab \
 	ggSpfToTab \
 	bedNamePickFirst \
-	bedBestTranscript
-
-
+	bedBestTranscript \
+	genePredToBed \
+	${USER_APP_SCRIPTS}
 
 # List of all directories to build
 
 ALL_APPS = $(UTILS_APPLIST) $(UCSC_APPS)
 
 # all: builds all utilities here
 
 all: $(ALL_APPS:%=%.all)
 
 %.all:
 	cd $* && echo $* && $(MAKE)
 
 # userAppsB: builds the user application specific programs
 # it would have been nice to be able to use the target name 'userApps'
 # here, but there is a directory by that name, and thus it always exists
 # and so the target does nothing.
 
-userAppsB: $(UTILS_APPLIST:%=%.userApps)
+userAppsB: $(UTILS_APPLIST:%=%.userApp) $(USER_APP_SCRIPTS:%=%.userAppScript)
 
-%.userApps:
+%.userApp:
 	cd $* && echo $* && $(MAKE)
 
+%.userAppScript:
+	@rm -f ${DESTDIR}${BINDIR}/$*
+	@if test -d $* ; \
+	then \
+	    chmod +x $*/$*; \
+	    echo cp -p $*/$* ${DESTDIR}${BINDIR}; \
+	    cp -p $*/$* ${DESTDIR}${BINDIR}; \
+	else \
+	    chmod +x $*; \
+	    echo cp -p $*/$* ${DESTDIR}${BINDIR}; \
+	    cp -p $* ${DESTDIR}${BINDIR}/$*; \
+	fi
+
 scripts: $(SCRIPT_FILES:%=%.scripts)
-	chmod +x genePredToBed/genePredToBed;
-	rm -f ${SCRIPTS}/genePredToBed;
-	echo cp -p genePredToBed/genePredToBed ${SCRIPTS};
-	@cp -p genePredToBed/genePredToBed ${SCRIPTS};
 
 %.scripts:
-	chmod +x $*
-	rm -f ${SCRIPTS}/$*
-	echo cp -p $* ${SCRIPTS}
-	cp -p $* ${SCRIPTS}
+	@rm -f ${SCRIPTS}/$*
+	@if test -d $* ; \
+	then \
+	    chmod +x $*/$*; \
+	    echo cp -p $*/$* ${SCRIPTS}; \
+	    cp -p $*/$* ${SCRIPTS}; \
+	else \
+	    chmod +x $*; \
+	    echo cp -p $* ${SCRIPTS}; \
+	    cp -p $* ${SCRIPTS}; \
+	fi
 
 testAll: $(ALL_APPS:%=%.testAll)
 
 %.testAll:
 	@test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true
 
 test: testAll
 	cd faToTwoBit && ${MAKE} test
 	cd twoBitToFa && ${MAKE} test
 	cd twoBitInfo && ${MAKE} test
 	cd bedGeneParts && ${MAKE} test
 
 clean: $(ALL_APPS:%=%.clean)
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 
 %.clean:
 	cd $* && echo $* && $(MAKE) clean
 
 BAD_DIRS= \
 	ccCpLock \
 	est2genomeToPsl \
 	geneStarts \
 	jimgrep \
 	jkShell \
 	dnsInfo \
 	wigAsciiToBinary \
 	cCp