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authorGeorge Hartzell <hartzell@alerce.com>2017-05-29 13:36:18 -0700
committerAdam J. Stewart <ajstewart426@gmail.com>2017-05-29 15:36:18 -0500
commit62daeaa525b1ae7b1f5da1c48d957430787be280 (patch)
tree7407481022af1fd10c2f1c7b2e9b2d51e1f83a95
parent7ea0e143c5e923b80b0c3fa3db321cc93adf02fd (diff)
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Add package for bamutil (#4387)
*Minimally* tested on CentOS 7. Stole the `install_target` bit from zip....
-rw-r--r--var/spack/repos/builtin/packages/bamutil/libstatgen-issue-9.patch11
-rw-r--r--var/spack/repos/builtin/packages/bamutil/package.py45
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)]