From 9e457049e450fce7547f90b033cd257bb793776c Mon Sep 17 00:00:00 2001
From: Eric Kow <eric.kow@gmail.com>
Date: Tue, 15 Apr 2014 13:23:07 +0100
Subject: [PATCH] megam: New package

Maximum Entropy (GA) Model Optimization Package
---
 .../science/misc/megam/default.nix            | 46 +++++++++++++++++++
 .../science/misc/megam/ocaml-3.12.patch       | 12 +++++
 .../science/misc/megam/ocaml-includes.patch   | 21 +++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 4 files changed, 81 insertions(+)
 create mode 100644 pkgs/applications/science/misc/megam/default.nix
 create mode 100644 pkgs/applications/science/misc/megam/ocaml-3.12.patch
 create mode 100644 pkgs/applications/science/misc/megam/ocaml-includes.patch

diff --git a/pkgs/applications/science/misc/megam/default.nix b/pkgs/applications/science/misc/megam/default.nix
new file mode 100644
index 000000000000..a0ee505dc97f
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/default.nix
@@ -0,0 +1,46 @@
+{ fetchurl, stdenv, ocaml, makeWrapper, ncurses }:
+
+let version = "0.92"; in
+stdenv.mkDerivation rec {
+  name = "megam-${version}";
+
+  src = fetchurl {
+    url = "http://hal3.name/megam/megam_src.tgz";
+    sha256 = "dc0e9f59ff8513449fe3bd40b260141f89c88a4edf6ddc8b8a394c758e49724e";
+  };
+
+  patches = [ ./ocaml-includes.patch ./ocaml-3.12.patch ];
+  
+  buildInputs = [ ocaml ncurses ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  makeFlags = "CAML_INCLUDES=${ocaml}/lib/ocaml/caml";
+
+  # see https://bugzilla.redhat.com/show_bug.cgi?id=435559
+  dontStrip = true;
+
+  installPhase = ''
+    mkdir -pv $out/bin
+    cp -Rv megam $out/bin
+  '';
+
+
+  meta = {
+    description = "MEGA Model Optimization Package";
+
+    longDescription =
+      ''  The software here is an implementation of maximum likelihood
+          and maximum a posterior optimization of the parameters of
+          these models.  The algorithms used are much more efficient
+          than the iterative scaling techniques used in almost every
+          other maxent package out there.  '';
+
+    homepage = http://www.umiacs.umd.edu/~hal/megam;
+
+    license = "non-commercial";
+
+    maintainers = [ ];
+    platforms = stdenv.lib.platforms.gnu;  # arbitrary choice
+  };
+}
diff --git a/pkgs/applications/science/misc/megam/ocaml-3.12.patch b/pkgs/applications/science/misc/megam/ocaml-3.12.patch
new file mode 100644
index 000000000000..8265acf6e4a7
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/ocaml-3.12.patch
@@ -0,0 +1,12 @@
+diff -ru megam_0.92/Makefile megam_0.92-b/Makefile
+--- megam_0.92/Makefile	2007-10-08 18:06:04.000000000 +0100
++++ megam_0.92-b/Makefile	2013-11-25 10:14:20.000000000 +0000
+@@ -59,7 +59,7 @@
+ 
+ WITHUNIX =unix.cma -cclib -lunix
+ 
+-WITHSTR =str.cma -cclib -lstr
++WITHSTR =str.cma -cclib -lcamlstr
+ 
+ WITHBIGARRAY =bigarray.cma -cclib -lbigarray
+ 
diff --git a/pkgs/applications/science/misc/megam/ocaml-includes.patch b/pkgs/applications/science/misc/megam/ocaml-includes.patch
new file mode 100644
index 000000000000..b3a56643448c
--- /dev/null
+++ b/pkgs/applications/science/misc/megam/ocaml-includes.patch
@@ -0,0 +1,21 @@
+diff -ru megam_0.92/Makefile megam_0.92-b/Makefile
+--- megam_0.92/Makefile	2007-10-08 18:06:04.000000000 +0100
++++ megam_0.92-b/Makefile	2013-11-25 10:14:20.000000000 +0000
+@@ -41,7 +41,7 @@
+ #
+ # The Caml compilers. #
+ # You may fix here the path to access the Caml compiler on your machine
+-CAMLC = ocamlc -g
++CAMLC = ocamlc -g $(WITHCLIBS)
+ CAMLOPT = ocamlopt -unsafe -ccopt -O4 -ccopt -ffast-math -inline 99999 
+ CAMLDEP = ocamldep
+ CAMLLEX = ocamllex
+@@ -70,7 +70,7 @@
+ WITHDBM =dbm.cma -cclib -lmldbm -cclib -lndbm
+ 
+ #WITHCLIBS =-I /usr/lib/ocaml/3.09.2/caml
+-WITHCLIBS =-I /usr/lib/ocaml/caml
++WITHCLIBS =-I $(CAML_INCLUDES) 
+ 
+ ################ End of user's variables #####################
+ 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 743d699ee876..9fdfda37a76b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -10352,6 +10352,8 @@ let
 
   golly = callPackage ../applications/science/misc/golly { };
 
+  megam = callPackage ../applications/science/misc/megam { };
+
   root = callPackage ../applications/science/misc/root { };
 
   simgrid = callPackage ../applications/science/misc/simgrid { };