remove submodules and simplify Makefile

.gitmodules

@@ -1,6 +0,0 @@
-[submodule "twt"]
-	path = twt
-	url = git://github.com/mlin/twt.git
-[submodule "CDE"]
-	path = CDE
-	url = git://github.com/mlin/CDE.git

Makefile

@@ -1,42 +1,20 @@
 all: PhyloCSF
 
-.PHONY: PhyloCSF CamlPaml twt cde-package clean
+.PHONY: PhyloCSF CamlPaml clean
 
 ARCH := $(shell uname).$(shell uname -m)
 PHYLOCSF_BASE := $(shell pwd)
 export PHYLOCSF_BASE
 
 PhyloCSF: CamlPaml
-	cd src; $(MAKE) clean; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS)
+	$(MAKE) -C src clean
+	$(MAKE) -C src $(MFLAGS)
 	cp src/_build/PhyloCSF.native PhyloCSF.$(ARCH)
 
-CamlPaml: twt/ocaml+twt
-	cd lib/CamlPaml; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS) reinstall
-
-twt/ocaml+twt: twt/ocaml+twt.ml
-	cd twt && $(MAKE)
-
-twt/ocaml+twt.ml:
-	git submodule update --init twt
-
-cde-package: PhyloCSF CDE/cde
-	rm -rf cde-package cde-package.$(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:
-	git submodule update --init CDE
-	cd CDE && $(MAKE)
+CamlPaml:
+	$(MAKE) -C lib/CamlPaml $(MFLAGS) reinstall
 	
 clean:
-	(cd CDE; $(MAKE) clean) || true
-	cd lib/CamlPaml; $(MAKE) clean
-	cd src; $(MAKE) clean
+	$(MAKE) -C lib/CamlPaml clean
+	$(MAKE) -C src clean
 	rm -f PhyloCSF.*
-	rm -rf cde-package*
-
-cleaner: clean
-	rm -rf twt CDE || true

cde.options

@@ -1,54 +0,0 @@
-# cde.options v1 (do not alter this first line!)
-
-# These directories often contain pseudo-files that shouldn't be tracked
-ignore_prefix=/dev/
-ignore_exact=/dev
-ignore_prefix=/proc/
-ignore_exact=/proc
-ignore_prefix=/sys/
-ignore_exact=/sys
-ignore_prefix=/var/cache/
-ignore_prefix=/var/lock/
-ignore_prefix=/var/log/
-ignore_prefix=/var/run/
-ignore_prefix=/var/tmp/
-ignore_prefix=/tmp/
-ignore_exact=/tmp
-
-# un-comment the entries below if you think they might help your app:
-#ignore_exact=/etc/ld.so.cache
-#ignore_exact=/etc/ld.so.preload
-#ignore_exact=/etc/ld.so.nohwcap
-
-# Ignore .Xauthority to allow X Windows programs to work
-ignore_substr=.Xauthority
-
-# Ignore so that networking can work properly
-ignore_exact=/etc/resolv.conf
-# These files might be useful to ignore along with /etc/resolv.conf
-# (un-comment if you want to try them)
-#ignore_exact=/etc/host.conf
-#ignore_exact=/etc/hosts
-#ignore_exact=/etc/nsswitch.conf
-#ignore_exact=/etc/gai.conf
-
-# Access the target machine's password files:
-# (some programs like texmacs need these lines to be commented-out,
-#  since they try to use home directory paths within the passwd file,
-#  and those paths might not exist within the package.)
-ignore_prefix=/etc/passwd
-ignore_prefix=/etc/shadow
-
-# These environment vars might lead to 'overfitting' and hinder portability
-ignore_environment_var=DBUS_SESSION_BUS_ADDRESS
-ignore_environment_var=ORBIT_SOCKETDIR
-ignore_environment_var=SESSION_MANAGER
-ignore_environment_var=XAUTHORITY
-ignore_environment_var=DISPLAY
-
-# For PhyloCSF: allow the dispatch script in our package to set PHYLOCSF_BASE
-# so that the parameters and examples can reside at the top level rather than
-# buried deep in cde-package/
-ignore_environment_var=PHYLOCSF_BASE
-ignore_prefix=/home/mlin/src/PhyloCSF/PhyloCSF_Examples
-ignore_prefix=/home/mlin/src/PhyloCSF/PhyloCSF_Parameters