From 70fe90f1ce47aeb722dd9343c69df66e9d7e1968 Mon Sep 17 00:00:00 2001
From: Mike Lin <mlin@mlin.net>
Date: Sat, 24 Mar 2012 01:08:10 -0400
Subject: [PATCH] Makefile section for building CDE package

---
 .gitmodules |  3 +++
 CDE         |  1 +
 Makefile    | 19 ++++++++++++++++---
 cde.options | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 74 insertions(+), 3 deletions(-)
 create mode 160000 CDE
 create mode 100644 cde.options

diff --git a/.gitmodules b/.gitmodules
index eb05e36..93325b2 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "twt"]
 	path = twt
 	url = git://github.com/mlin/twt.git
+[submodule "CDE"]
+	path = CDE
+	url = git://github.com/pgbovine/CDE.git
diff --git a/CDE b/CDE
new file mode 160000
index 0000000..36f9f2f
--- /dev/null
+++ b/CDE
@@ -0,0 +1 @@
+Subproject commit 36f9f2f1057545b3b7ec7f8570b6c6dca4c5dcd2
diff --git a/Makefile b/Makefile
index a45ca78..b57daba 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,10 @@
 all: PhyloCSF
 
-.PHONY: PhyloCSF CamlPaml clean
+.PHONY: PhyloCSF CamlPaml cde-package CDE clean
 
-ARCH := `uname`.`uname -m`
-export ARCH
+ARCH := $(shell uname).$(shell uname -m)
+PHYLOCSF_BASE := $(shell pwd)
+export PHYLOCSF_BASE
 
 PhyloCSF: CamlPaml
 	cd src; $(MAKE) clean; $(MAKE) $(MFLAGS)
@@ -12,7 +13,19 @@ PhyloCSF: CamlPaml
 CamlPaml: 
 	cd lib/CamlPaml; $(MAKE) $(MFLAGS) reinstall
 
+cde-package: PhyloCSF CDE
+	CDE/cde ./PhyloCSF.$(ARCH) 12flies PhyloCSF_Examples/tal-AA.fa 
+	CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3
+	#CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --frames=3 --removeRefGaps --aa
+	mv cde-package cde-package.$(ARCH)
+	tar -cf cde-package.$(ARCH).tar cde-package.$(ARCH)
+
+CDE:
+	cd CDE && make
+
 clean:
 	cd lib/CamlPaml; $(MAKE) clean
 	cd src; $(MAKE) clean
 	rm -f PhyloCSF.*
+	rm -rf cde-package*
+	cd CDE && make clean || true
\ No newline at end of file
diff --git a/cde.options b/cde.options
new file mode 100644
index 0000000..4826b09
--- /dev/null
+++ b/cde.options
@@ -0,0 +1,54 @@
+# 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