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author | George Hartzell <hartzell@alerce.com> | 2017-05-29 13:36:18 -0700 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-05-29 15:36:18 -0500 |
commit | 62daeaa525b1ae7b1f5da1c48d957430787be280 (patch) | |
tree | 7407481022af1fd10c2f1c7b2e9b2d51e1f83a95 | |
parent | 7ea0e143c5e923b80b0c3fa3db321cc93adf02fd (diff) | |
download | spack-62daeaa525b1ae7b1f5da1c48d957430787be280.tar.gz spack-62daeaa525b1ae7b1f5da1c48d957430787be280.tar.bz2 spack-62daeaa525b1ae7b1f5da1c48d957430787be280.tar.xz spack-62daeaa525b1ae7b1f5da1c48d957430787be280.zip |
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.patch | 11 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/bamutil/package.py | 45 |
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)] |