ghmm: Initial packaging including split off python2 interface

pkgs/all-packages.nix

@@ -15,6 +15,8 @@ self: super: pkgs: with pkgs; {
 
   #firedrake = callPackage ./firedrake { };
 
+  ghmm = callPackage ./ghmm { };
+
   inherit (callPackages ./octopus/libxc.nix { }) libxc301 libxc404;
   libxc3 = libxc301;
   libxc4 = libxc404;

pkgs/ghmm/default.nix

@@ -0,0 +1,56 @@
+{ stdenv, fetchsvn, autoreconfHook, pkgconfig
+, libxml2, python2Packages, swig }:
+
+stdenv.mkDerivation rec {
+  name = "ghmm-svn${version}";
+  version = "2341";
+
+  src = fetchsvn {
+    url = "https://svn.code.sf.net/p/ghmm/code/trunk/ghmm";
+    rev = "${version}";
+    sha256 = "067anx9mhs0f4f38q4wj2fds1pkp0jcy10i0fhggvrcp31gy0329";
+  };
+
+  #patches = [ ./static-lib-for-tools.patch ];
+  postPatch = ''
+    sed -i -e 's,\(LDADD = .*/ghmm/\.libs/libghmm\)\.a,\1.la,' */Makefile.am
+  '';
+
+  # The python wrapper needs to be built here for dependencies
+  outputs = [ "out" "py" ];
+
+  configureFlags = [
+    "--without-python"
+  ];
+
+  postBuild = ''
+    cd ghmmwrapper
+    python setup.py build
+    cd ..
+  '';
+
+  postInstall = ''
+    cd ghmmwrapper
+    python setup.py install --prefix="$py"
+    cd ..
+  '';
+
+  buildInputs = [
+    autoreconfHook
+    pkgconfig
+    libxml2
+    python2Packages.python
+    swig
+  ];
+
+  hardeningDisable = [ "format" ];
+
+  meta = with stdenv.lib; {
+    description = "The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.";
+    homepage = http://ghmm.sourceforge.net;
+    platforms = platforms.all;
+    license = licenses.lgpl2Plus;
+  };
+
+  enableParallelBuilding = true;
+}

pkgs/ghmm/static-lib-for-tools.patch

@@ -0,0 +1,60 @@
+--- ghmm-r2341/ghmm/Makefile.am	1969-12-31 19:00:01.000000000 -0500
++++ ghmm-r2341/ghmm/Makefile.am_	2019-04-30 17:11:30.975676919 -0400
+@@ -128,6 +128,57 @@
+ 		    block_compression.c block_compression.h
+ 
+ 
++noinst_LIBRARIES = libghmm.a
++
++libghmm_a_CFLAGS = $(AM_CFLAGS)
++libghmm_a_SOURCES= ghmm.h \
++		   ghmmconfig.h \
++                   rng.c rng.h \
++                   randvar.c randvar.h \
++                   matrixop.c matrixop.h \
++                   gauss_tail.c \
++                   mes.c mes.h \
++                   ghmm_internals.c ghmm_internals.h \
++                   mprintf.c mprintf.h \
++                   vector.c vector.h \
++                   matrix.c  matrix.h \
++                   scanner.c scanner.h \
++                   linkedlist.c \
++                   sequence.c sequence.h \
++                   psequence.c psequence.h \
++                   xmlreader.c xmlreader.h \
++                   xmlwriter.c xmlwriter.h \
++                   model.c model.h \
++                   foba.c foba.h \
++                   viterbi.c viterbi.h \
++                   reestimate.c reestimate.h \
++                   gradescent.c gradescent.h \
++                   kbest.c kbest.h \
++                   discrime.c discrime.h \
++                   modelutil.c \
++                   cluster.c cluster.h \
++                   root_finder.c \
++                   smodel.c smodel.h \
++                   sfoba.c sfoba.h \
++                   sviterbi.c sviterbi.h \
++                   sreestimate.c sreestimate.h \
++                   scluster.c scluster.h \
++                   sgenerate.c sgenerate.h \
++                   smixturehmm.c smixturehmm.h \
++                   smap_classify.c smap_classify.h \
++                   sdmodel.c sdmodel.h \
++                   sdfoba.c sdfoba.h \
++                   sdviterbi.c \
++                   pmodel.c pmodel.h \
++                   pviterbi.c pviterbi.h \
++                   pviterbi_propagate.c pviterbi_propagate.h \
++                   fbgibbs.c fbgibbs.h \
++                   cfbgibbs.c cfbgibbs.h \
++		   bayesian_hmm.c bayesian_hmm.h \
++		   continuous_fbgibbs.c continuous_fbgibbs.h \
++		   block_compression.c block_compression.h
++
++
+ pkginclude_HEADERS = ghmm.h \
+ 		  ghmmconfig.h \
+                   sequence.h \

pkgs/python-packages.nix

@@ -1,5 +1,7 @@
 pkgs: self: super: with self; {
 
+  ghmm = disabledIf isPy3k ( toPythonModule (pkgs.ghmm.override { python2Packages=self; }) ).py;
+
   openslide = callPackage ./openslide/python.nix { openslide = pkgs.openslide; };
 
   pybedtools = callPackage ./pybedtools.nix { };