adaefb41c47c8ed44b75ad2793770bae5070e71b
hiram
  Fri Jun 18 20:36:26 2010 -0700
last bunch of makefiles that need a clean target
diff --git src/shortReads/makefile src/shortReads/makefile
index d6d14c0..84e1dc1 100644
--- src/shortReads/makefile
+++ src/shortReads/makefile
@@ -1,27 +1,40 @@
 include ../inc/common.mk
 
-all:
-	cd bfastMafFix && ${MAKE}
-	cd bwtFind && ${MAKE}
-	cd bwtMake && ${MAKE}
-	cd bwtReverse && ${MAKE}
-	cd elandToSplat && ${MAKE}
-	cd i16Find && ${MAKE}
-	cd itsaDump && ${MAKE}
-	cd itsaFind && ${MAKE}
-	cd itsaMake && ${MAKE}
-	cd shortRepeatFind && ${MAKE}
-	cd shortRepeatMerge && ${MAKE}
-	cd splat && ${MAKE}
-	cd splatCheck1 && ${MAKE}
-	cd splatCheck2 && ${MAKE}
-	cd splatMerge && ${MAKE}
-	cd splatTestSet && ${MAKE}
-	cd splatToEland && ${MAKE}
-	cd splixMake && ${MAKE}
-	cd sufaFind && ${MAKE}
-	cd sufaMake && ${MAKE}
-	cd sufaRepeatFind && ${MAKE}
-	cd sufxDump && ${MAKE}
-	cd sufxFind && ${MAKE}
-	cd sufxMake && ${MAKE}
+# List of directories to build
+USE_DIRS = $(DIRS)
+
+DIRS = \
+	bfastMafFix \
+	bwtFind \
+	bwtMake \
+	bwtReverse \
+	elandToSpl \
+	i16Find \
+	itsaDump \
+	itsaFind \
+	itsaMake \
+	shortRepeatFind \
+	shortRepeatMerge \
+	splat \
+	splatCheck1 \
+	splatCheck2 \
+	splatMerge \
+	splatTestSet \
+	splatToEland \
+	splixMake \
+	sufaFind \
+	sufaMake \
+	sufaRepeatFind \
+	sufxDump \
+	sufxFind \
+	sufxMake
+
+all: $(USE_DIRS:%=%.all)
+
+%.all:
+	( cd $* && echo $* && $(MAKE) )
+
+clean:: $(USE_DIRS:%=%.clean)
+
+%.clean::
+	( cd $* && echo $* && $(MAKE) clean )