Add package for bamutil (#4387)

*Minimally* tested on CentOS 7.

Stole the `install_target` bit from zip....

2 files changed, 56 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-9.patch b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-9.patch
new file mode 100644
index 0000000000..23435f7c3c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-9.patch
@@ -0,0 +1,11 @@
+--- a/libStatGen/general/PedigreeLoader.cpp	2017-05-29 11:08:07.627528417 -0700
++++ b/libStatGen/general/PedigreeLoader.cpp	2017-05-29 11:08:36.247547411 -0700
+@@ -636,7 +636,7 @@
+             return 2;
+         default :
+         {
+-            bool result = atoi(code);
++            int result = atoi(code);
+ 
+             if (result != 0 && result != 1 && result != 2)
+             {
diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py
new file mode 100644
index 0000000000..1c1268f7f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamutil/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 Bamutil(MakefilePackage):
+    """bamUtil is a repository that contains several programs
+       that perform operations on SAM/BAM files. All of these programs
+       are built into a single executable, bam.
+    """
+
+    homepage = "http://genome.sph.umich.edu/wiki/BamUtil"
+    url      = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
+
+    version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
+
+    # Looks like this will be fixed in 1.0.14.
+    # https://github.com/statgen/libStatGen/issues/9
+    patch('libstatgen-issue-9.patch', when='@1.0.13:')
+
+    @property
+    def install_targets(self):
+        return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]