From bd3f981fbbbcedf330eb836a57b7b4c2f4755558 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?=
 <weijianwen@gmail.com>
Date: Mon, 2 Jul 2018 20:54:41 +0800
Subject: [PATCH] A new package: xhmm. (#8620)

* A new package: xhmm.

* Flake8.

* Support general BLAS.
---
 .../repos/builtin/packages/xhmm/package.py    | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/xhmm/package.py

diff --git a/var/spack/repos/builtin/packages/xhmm/package.py b/var/spack/repos/builtin/packages/xhmm/package.py
new file mode 100644
index 0000000000..e85102daeb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xhmm/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Xhmm(MakefilePackage):
+    """The XHMM C++ software suite was written to
+    call copy number variation (CNV) from next-generation
+    sequencing projects, where exome capture was used
+    (or targeted sequencing, more generally)."""
+
+    homepage = "http://atgu.mgh.harvard.edu/xhmm/index.shtml"
+    url      = "https://bitbucket.org/statgen/xhmm.git"
+
+    version('20160104', git='https://bitbucket.org/statgen/xhmm.git',
+            commit='cc14e528d90932f059ac4fe94e869e81221fd732')
+
+    depends_on('lapack')
+
+    def edit(self, spec, prefix):
+        filter_file('GCC', 'CC', 'sources/hmm++/config_rules.Makefile')
+        filter_file('GCC =gcc', '', 'sources/hmm++/config_defs.Makefile')
+
+    def build(self, spec, prefix):
+        make('LAPACK_LIBS=%s' % ''.join(spec['lapack'].libs.names))
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('xhmm', prefix.bin)