From 0137f17306abd4d3969cee6db1fce8290674a1ff Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 9 Aug 2017 15:39:37 -0500 Subject: shapeit: new package (#5042) * shapeit: new package * fixing versioning --- .../repos/builtin/packages/shapeit/package.py | 44 ++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/shapeit/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/shapeit/package.py b/var/spack/repos/builtin/packages/shapeit/package.py new file mode 100644 index 0000000000..a3f79c6255 --- /dev/null +++ b/var/spack/repos/builtin/packages/shapeit/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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) -- cgit v1.2.3-60-g2f50