From 96f976920c3d7a53e6942665bb2bb27f163859a7 Mon Sep 17 00:00:00 2001
From: Mike Lin <mlin@mlin.net>
Date: Sat, 22 Sep 2012 14:32:49 -0700
Subject: [PATCH] Makefile: tweak dependencies

---
 Makefile | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/Makefile b/Makefile
index b22a1b7..a43917e 100644
--- a/Makefile
+++ b/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)
@@ -10,14 +10,16 @@ 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.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3 --allScores
@@ -25,10 +27,10 @@ cde-package: PhyloCSF CDE
 	mv cde-package cde-package.$(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