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shapeit: new package (#5042)

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* shapeit: new package

* fixing versioning
This commit is contained in:
Audrey Thoma 2017-08-09 15:39:37 -05:00 committed by Adam J. Stewart
parent 1f578c5777
commit 0137f17306
1 changed files with 44 additions and 0 deletions
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var/spack/repos/builtin/packages/shapeit/package.py Normal file
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##############################################################################
# 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 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 Shapeit(Package):
"""SHAPEIT is a fast and accurate method for estimation of haplotypes (aka
phasing) from genotype or sequencing data."""
homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html"
url = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.dynamic.tgz"
version('2.837', '895873bb655a0a985cbfd870fdd1dd60')
def url_for_version(self, version):
url = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v{0}.r{1}.GLIBCv2.12.Linux.dynamic.tgz'
return url.format(version[0], version[1])
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('bin'):
install('shapeit', prefix.bin)