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authormanifest <robqiao@users.noreply.github.com>2020-06-25 18:13:33 +0930
committerGitHub <noreply@github.com>2020-06-25 10:43:33 +0200
commit5c712a03a1262b97fc920c86a2125fef7c806762 (patch)
tree5fc10772c0331607eae00625975953db75c2a05a /var
parentb26e93af3d19e4492cf049bc7479eb85bc8f7da7 (diff)
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msmc2: added package at v2.1.2 (#17170)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/msmc2/package.py43
1 files changed, 43 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/msmc2/package.py b/var/spack/repos/builtin/packages/msmc2/package.py
new file mode 100644
index 0000000000..efd0bec341
--- /dev/null
+++ b/var/spack/repos/builtin/packages/msmc2/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2020 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 Msmc2(MakefilePackage):
+ """
+ This program implements MSMC2, a method to infer population size history
+ and population separation history from whole genome sequencing data.
+ """
+
+ homepage = "https://github.com/stschiff/msmc2"
+ url = "https://github.com/stschiff/msmc2/archive/v2.1.1.tar.gz"
+
+ maintainers = ['robqiao']
+
+ version('2.1.2', sha256='c8c2b6ed6ef1b5d6e6e15ec0d968288e5bdae2bea1f3b4ec790f599e96bb26cd')
+ version('2.1.1', sha256='151dd75a8b0371ff94eed9504a7a73a2924e10466de30c230c1bb3c35a1a0913')
+ version('2.0.2', sha256='91152b2494342148ff84a1e5c6d2f5f0d53acba12722cd68ff5807ba4e82af55')
+ version('2.0.1', sha256='97e859e6f08689baf29d3c61b6904cfa5a292f8ce7b3532e055ce3047d8472f4')
+ version('2.0.0', sha256='9de38239f6e729a0f6f492ca671e2e70541eb5db558d816e64184c06611a1c7e')
+
+ depends_on('gsl', type=('build', 'run'))
+ depends_on('dmd@:2.081.0', type='build')
+
+ def edit(self, spec, prefix):
+ # Set DMD compiler
+ filter_file('dmd',
+ join_path(self.spec['dmd'].prefix.linux.bin64, 'dmd'),
+ 'Makefile', string=True)
+
+ gsllibdir = spec['gsl'].libs.directories[0]
+
+ # Set GSLDIR
+ filter_file('GSLDIR=/usr/local/lib',
+ 'GSLDIR={0}'.format(gsllibdir),
+ 'Makefile', string=True)
+
+ def install(self, spec, prefix):
+ install_tree('build/release', prefix.bin)