New package: EEM (#12321)

var/spack/repos/builtin/packages/eem/add_include.patch

@@ -0,0 +1,22 @@
+diff -ruN eemParallel_1.0.1.org/src/utility/Date.cpp eemParallel_1.0.1/src/utility/Date.cpp
+--- eemParallel_1.0.1.org/src/utility/Date.cpp	2014-07-20 21:48:22.000000000 +0900
++++ eemParallel_1.0.1/src/utility/Date.cpp	2019-08-08 09:58:18.768020679 +0900
+@@ -7,6 +7,7 @@
+ #include <sys/types.h>
+ #include <iostream>
+ #include <sstream>
++#include <ctime>
+ #endif
+ 
+ #ifdef VC
+diff -ruN eemParallel_1.0.1.org/src/utility/MyFunc.cpp eemParallel_1.0.1/src/utility/MyFunc.cpp
+--- eemParallel_1.0.1.org/src/utility/MyFunc.cpp	2014-07-20 21:48:22.000000000 +0900
++++ eemParallel_1.0.1/src/utility/MyFunc.cpp	2019-08-08 09:57:58.945943754 +0900
+@@ -11,6 +11,7 @@
+ #include <iomanip>
+ #include <cmath>
+ #include <cassert>
++#include <random>
+ 
+ #include "HypergeometricDistributionImpl.h"
+ 

var/spack/repos/builtin/packages/eem/package.py

@@ -0,0 +1,40 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Eem(MakefilePackage):
+    """EEM is a program to extract the gene group and expression modules
+       that are co-expressed in the mRNA expression data."""
+
+    homepage = "http://www.scls.riken.jp/scruise/software/eem.html"
+    url      = "http://www.scls.riken.jp/wp-content/uploads/2014/07/eemParallel_1.0.1.tar.gz"
+
+    version('1.0.1', sha256='f617ea7350fce3b2581c814f70bda4427cbab83aac54a2dcadb36e8193f300bb')
+
+    variant('K', default=False, description='Build for K computer')
+
+    phases = ['edit', 'install']
+
+    depends_on('mpi')
+
+    build_directory = 'src'
+
+    patch('add_include.patch')
+
+    def edit(self, spec, prefix):
+        settings = FileFilter('./src/local_settings.mk')
+
+        settings.filter('$(HOME)/local', prefix, string=True)
+        settings.filter('mpicxx', self.spec['mpi'].mpicxx, string=True)
+
+        if '+K' in self.spec:
+            settings.filter('CXXFLAGS= -Wall -Wno-sign-compare -g',
+                            'CXXFLAGS=', string=True)
+            settings.filter('CXXFLAGS+= -std=c++11 -DHAVE_UNORDERED_MAP',
+                            'CXXFLAGS+= -DHAVE_UNORDERED_MAP', string=True)
+            settings.filter('CXXFLAGS+= -DHAVE_SHUFFLE',
+                            '#CXXFLAGS+= -DHAVE_SHUFFLE', string=True)