Merge branch 'master' of github.com:mlin/PhyloCSF

.gitmodules

@@ -1,3 +1,6 @@
-[submodule "ocaml+twt"]
-	path = ocaml+twt
+[submodule "twt"]
+	path = twt
 	url = git://github.com/mlin/twt.git
+[submodule "CDE"]
+	path = CDE
+	url = git://github.com/pgbovine/CDE.git

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

README

@@ -9,35 +9,78 @@
 |                 http://compbio.mit.edu/PhyloCSF                     | 
 +---------------------------------------------------------------------+
 
-
 SOURCE DISTRIBUTION
 
-Compiling PhyloCSF from source may be difficult for most users,
-because it requires an Objective Caml toolchain that's probably not
-already present on your system. For this reason, we provide
-precompiled binaries for Linux and Mac OS X on our website.
+Please see our web site for more information about PhyloCSF. Compiling
+this software from source may be difficult for most users, because it
+requires an Objective Caml toolchain that's probably not already
+present on your system. For this reason, we provide digitally-signed
+32-bit and 64-bit Linux executables on our web site.
+
+The source distribution is divided into a library, CamlPaml, containing
+generic infrastructure for phylogenetic rate models, and a program
+implementing the PhyloCSF-specific models and driver program. With
+additional development, the CamlPaml library will eventually be
+released as a separate entity, but for now it is just part of this
+distribution.
+
+Here are the steps to build the source:
+
+[1A] Install various dependencies (Ubuntu 11.10+)
 
-DEPENDENCIES
+Install these packages using apt-get:
+ocaml-findlib libocamlgsl-ocaml-dev libbatteries-ocaml-dev make
+
+[1B] Install various dependencies (other Linux, Mac OS X)
 
 - GNU Scientific Library 
 * Objective Caml 3.11+, with native code compiler
-* findlib
+* OCaml findlib
 * OCaml Batteries Included 1.20+
 * ocamlgsl 0.60+
-- ocaml+twt 0.92+ http://people.csail.mit.edu/mikelin/ocaml+twt/
 
 * These can be set up using GODI: http://godi.camlcity.org/
 
-The source distribution is divided into a library, CamlPaml,
-containing generic infrastructure for phylogenetic rate models, and a
-program implementing the PhyloCSF-specific models and driver
-program. With additional development, the CamlPaml library will
-eventually be released as a separate entity, but for now it is just
-part of this distribution.
+[2] Configure OCaml findlib
+
+If you installed findlib (OCaml's package manager) using the Ubuntu
+packages, or any other method that led to system-wide installation, you
+must set some environment variables to make it use a directory to which
+you have write access. (Alternatively, you can complete the subsequent
+steps as root, e.g. using sudo)
+
+  mkdir -p $HOME/opt/lib/ocaml                     # or whatever
+  export OCAMLPATH=$HOME/opt/lib/ocaml:$OCAMLPATH
+  export OCAMLFIND_DESTDIR=$OCAMLPATH
+
+To verify your configuration, run
+
+  ocamlfind printconf
+
+"Packages will be installed in" should be a directory you can write to,
+and that same directory should appear in "Search path".
+
+[3] Install ocaml+twt
+
+The code is written in a dialect of OCaml for which you must install a
+preprocessor from: http://people.csail.mit.edu/mikelin/ocaml+twt/
+Download the tarball, extract it, and run
+
+  make install INSTALLDIR=$HOME/directory/in/your/PATH
+    -or-
+  sudo make install
+
+If you obtained this PhyloCSF source distribution by cloning the git
+repository, ocaml+twt is available as a submodule. You can run
+
+  git submodule init
+  git submodule update
+  cd twt
+
+and then one of the above 'make install' commands.
 
-COMPILING
+[4] Compile PhyloCSF
 
-Assuming the above dependencies are satisfied, just run `make` in this
-directory. This will build and install the CamlPaml library, then
-compile the PhyloCSF executable and copy it to PhyloCSF.ARCH in this
-directory, where e.g. ARCH = Linux.x86_64.
+Now just run 'make' in this directory. This will build and install the
+CamlPaml library, then compile the PhyloCSF executable and copy it to
+PhyloCSF.ARCH in this directory, where e.g. ARCH = Linux.x86_64.

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