Makefile: tweak dependencies

Makefile

@@ -1,6 +1,6 @@
 all: PhyloCSF
 
-.PHONY: PhyloCSF CamlPaml twt cde-package CDE clean
+.PHONY: PhyloCSF CamlPaml twt cde-package clean
 
 ARCH := $(shell uname).$(shell uname -m)
 PHYLOCSF_BASE := $(shell pwd)
@@ -10,25 +10,27 @@ PhyloCSF: CamlPaml
 	cd src; $(MAKE) clean; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS)
 	cp src/_build/PhyloCSF.native PhyloCSF.$(ARCH)
 
-CamlPaml: twt
+CamlPaml: twt/ocaml+twt
 	cd lib/CamlPaml; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS) reinstall
 
-twt:
-	git submodule update --init twt
+twt/ocaml+twt: twt/ocaml+twt.ml
 	cd twt && $(MAKE)
 
-cde-package: PhyloCSF CDE
+twt/ocaml+twt.ml:
+	git submodule update --init twt
+
+cde-package: PhyloCSF CDE/cde
 	rm -rf cde-package cde-package.$(ARCH)
 	CDE/cde ./PhyloCSF.$(ARCH) 12flies PhyloCSF_Examples/tal-AA.fa 
 	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3 --allScores
 	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --strategy=fixed --frames=3 --orf=ATGStop --minCodons=400 --allScores --removeRefGaps --aa
 	mv cde-package cde-package.$(ARCH)
 	tar -cf cde-package.$(ARCH).tar cde-package.$(ARCH)	
 
-CDE:
+CDE/cde:
 	git submodule update --init CDE
 	cd CDE && $(MAKE)
-
+	
 clean:
 	cd lib/CamlPaml; $(MAKE) clean
 	cd src; $(MAKE) clean