257675a4fe52badf7773d16e3bc788c61cae5a0d
braney
  Wed Jan 12 12:49:50 2011 -0800
fix up some misunderstanding about where the gtf utilities live
diff --git src/makefile src/makefile
index 79516ea..5f48851 100644
--- src/makefile
+++ src/makefile
@@ -1,152 +1,154 @@
 include inc/common.mk
 
 
 all: utils cgi blatSuite
 
 alpha: clean utils-alpha cgi-alpha blatSuite
 
 beta: check-beta clean cgi-beta
 
 # do a git update and clean
 update:
 	git pull
 	${MAKE} clean
 
 topLibs:
 	@./machTest.sh
 	cd lib && ${MAKE}
 	cd jkOwnLib && ${MAKE}
 
 hgLib:
 	@./hg/sqlEnvTest.sh
 	cd hg/lib && ${MAKE}
 
 libs: topLibs hgLib
 	cd hg/protein/lib && ${MAKE}
 
 cgi: libs
 	cd hg && ${MAKE} cgi
 
 cgi-alpha: libs
 	cd hg && ${MAKE} alpha
 
 cgi-beta: check-beta libs
 	cd hg && ${MAKE} beta
 
 check-beta:
 	# this will fail if we are not in a beta checkout:
 	git branch | egrep 'v[0-9]+_branch' > /dev/null	
 
 blatSuite: topLibs 
 	cd blat && ${MAKE}
 	cd gfClient && ${MAKE}
 	cd gfServer && ${MAKE}
 	cd webBlat && ${MAKE}
 	cd hg/pslPretty && ${MAKE}
 	cd hg/pslReps && ${MAKE}
 	cd hg/pslSort && ${MAKE}
 	cd utils/nibFrag && ${MAKE}
 	cd utils/faToNib && ${MAKE}
 	cd utils/faToTwoBit && ${MAKE}
 	cd utils/twoBitToFa && ${MAKE}
 	cd utils/twoBitInfo && ${MAKE}
 	cd isPcr && ${MAKE}
 	cd blatz && ${MAKE}
 
 # all of these application makefiles have been updated to include use
 #	of DESTDIR and BINDIR
 
 UTILS_APPLIST = bedClip bedGraphToBigWig bedToBigBed \
         bigBedInfo bigBedSummary bigBedToBed \
 	bigWigInfo bigWigSummary bigWigToBedGraph bigWigToWig\
 	faCount faFrag faOneRecord faRandomize faSize faSomeRecords faToNib \
 	faToTwoBit htmlCheck nibFrag stringify \
 	textHistogram twoBitInfo twoBitToFa userApps wigCorrelate wigToBigWig
 
 HG_APPLIST = bedSort liftUp liftOver bedItemOverlapCount encode/validateFiles \
-	 gtfToGenePred ratStuff/mafsInRegion ratStuff/mafSpeciesSubset pslCDnaFilter
+	 ratStuff/mafsInRegion ratStuff/mafSpeciesSubset \
+	 pslCDnaFilter genePredToGtf
 
-HG_UTILS_APPLIST = bedExtendRanges gff3ToGenePred overlapSelect
+
+HG_UTILS_APPLIST = bedExtendRanges gff3ToGenePred gtfToGenePred overlapSelect
 
 userApps: topLibs hgLib
 	@for P in ${UTILS_APPLIST}; do \
 	    ( cd utils/$${P} && echo utils/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_APPLIST}; do \
 	    ( cd hg/$${P} && echo hg/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_UTILS_APPLIST}; do \
 	    ( cd hg/utils/$${P} && echo hg/utils/$${P} && ${MAKE} ) ; \
 	done
 
 clean:
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} clean ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd lib && ${MAKE} clean 
 	cd hg && ${MAKE} clean
 	cd hg && ${MAKE} clean_utils
 	cd jkOwnLib && ${MAKE} clean
 	cd utils && ${MAKE} clean
 	cd webBlat && ${MAKE} clean
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 	rm -f tags TAGS
 
 testDirs = lib blat gfServer hg
 test:: $(testDirs:%=%.test)
 %.test:
 	cd $* && ${MAKE} test
 
 LIB_TAGS_IN = lib/*.[hc] hg/lib/*.[hc] jkOwnLib/*.c inc/*.h hg/inc/*.h
 
 # build tags for libraries
 .PHONY: tags
 tags:
 	ctags ${LIB_TAGS_IN}
 
 # build emacs tags for libraries
 .PHONY: etags
 etags:
 	etags ${LIB_TAGS_IN}
 
 # build tags for all files
 .PHONY: tags-all
 tags-all:
 	find . -name '*.[ch]' | ctags -L -
 
 # build emacs tags for all files
 .PHONY: etags-all
 etags-all:
 	find . -name '*.[ch]' | etags -
 
 utils: libs
 	${MKDIR} ${SCRIPTS}
 	${MKDIR} ${DESTDIR}${BINDIR}
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd utils && ${MAKE}
 	cd hg && ${MAKE} utils
 
 utils-alpha: libs
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd utils && ${MAKE} alpha
 	cd hg && ${MAKE} utils
 
 DIRS = ameme blat cdnaAli index reformat xenoAli \
        dnaDust protDust idbQuery scanIntrons tracks weblet \
        aladdin getgene primeMate wormAli fuse