58e25c03395494013032de03317630e411f43bb9
braney
  Mon Mar 28 14:58:35 2011 -0700
fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps  #3152
diff --git src/makefile src/makefile
index d685fda..21d4487 100644
--- src/makefile
+++ src/makefile
@@ -47,56 +47,62 @@
 	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 \
+	faCount faFrag faOneRecord faPolyASizes faRandomize faSize \
+	faSomeRecords faToNib \
 	faToTwoBit htmlCheck nibFrag paraFetch paraSync sizeof stringify \
 	textHistogram twoBitInfo twoBitToFa userApps wigCorrelate wigToBigWig
 
 HG_APPLIST = bedSort liftUp liftOver bedItemOverlapCount encode/validateFiles \
 	 ratStuff/mafsInRegion ratStuff/mafSpeciesSubset \
-	 pslCDnaFilter genePredToGtf
+	 pslCDnaFilter genePredToGtf pslPretty pslReps pslSort 
 
 
 HG_UTILS_APPLIST = bedExtendRanges gff3ToGenePred gtfToGenePred overlapSelect
 
 HG_HGWIGGLE_APP = hgWiggle
 
+BLAT_APPLIST = blat gfClient gfServer 
+
 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
 	@for P in ${HG_HGWIGGLE_APP}; do \
 	    ( cd hg/makeDb/hgLoadWiggle && echo hg/makeDb/hgLoadWiggle && ${MAKE} $${P} ) ; \
 	done
+	@for P in ${BLAT_APPLIST}; do \
+	    ( cd $${P} && echo $${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
 	cd isPcr && ${MAKE} clean