new package: msmc (starting at 1.1.0) (#9654)

1 files changed, 34 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/msmc/package.py b/var/spack/repos/builtin/packages/msmc/package.py
new file mode 100644
index 0000000000..7acde0f400
--- /dev/null
+++ b/var/spack/repos/builtin/packages/msmc/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 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 Msmc(MakefilePackage):
+    """This software implements MSMC, a method to infer population size
+       and gene flow from multiple genome sequences"""
+
+    homepage = "https://github.com/stschiff/msmc"
+    url      = "https://github.com/stschiff/msmc/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', sha256='989064400fe392ca3d2ac1a253ce7edf1801b6a7eeb77bbf2ff7bf67910216c4')
+
+    depends_on('gsl', type=('build', 'run'))
+    depends_on('dmd', type='build')
+
+    def edit(self, spec, prefix):
+        filter_file('dmd',
+                    join_path(self.spec['dmd'].prefix.linux.bin64, 'dmd'),
+                    'Makefile', string=True)
+
+    def build(self, spec, prefix):
+        gsllibdir = self.spec['gsl'].prefix.lib
+        libgsl = join_path(gsllibdir, 'libgsl.a')
+        libgslcblas = join_path(gsllibdir, 'libgslcblas.a')
+        make('GSL={0} {1}'.format(libgsl, libgslcblas))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('build', prefix.bin)