From 5fb23b21e01c6c22b7c355d53e4d1b8c786faaa2 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Fri, 18 Aug 2017 09:36:19 -0500 Subject: vegas2: new package (#5150) * vegas2: new package * small version things --- var/spack/repos/builtin/packages/plink/package.py | 41 ++++++++++++++++++ .../repos/builtin/packages/r-corpcor/package.py | 34 +++++++++++++++ .../repos/builtin/packages/r-mvtnorm/package.py | 3 +- var/spack/repos/builtin/packages/vegas2/package.py | 49 ++++++++++++++++++++++ 4 files changed, 126 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/plink/package.py create mode 100644 var/spack/repos/builtin/packages/r-corpcor/package.py create mode 100644 var/spack/repos/builtin/packages/vegas2/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py new file mode 100644 index 0000000000..a519f30184 --- /dev/null +++ b/var/spack/repos/builtin/packages/plink/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 Plink(Package): + """PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a + computationally efficient manner.""" + + homepage = "https://www.cog-genomics.org/plink/1.9/" + + version('1.9', 'a2325881594856c0f1b7523290d1e04f', + url='https://www.cog-genomics.org/static/bin/plink170815/plink_linux_x86_64.zip') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('plink', prefix.bin) + install('prettify', prefix.bin) diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py new file mode 100644 index 0000000000..09798cbd2d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -0,0 +1,34 @@ +############################################################################## +# 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 RCorpcor(RPackage): + """Efficient Estimation of Covariance and (Partial) Correlation""" + + homepage = "https://cran.r-project.org/package=corpcor" + url = "https://cran.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" + + version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925') diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index 31933e70a3..2df9206a63 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -30,6 +30,7 @@ class RMvtnorm(RPackage): deviates and densities.""" homepage = "http://mvtnorm.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz" + url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz" + version('1.0-6', 'cb69426868fd3e330412b8491901d9d4') version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py new file mode 100644 index 0000000000..1c091a568c --- /dev/null +++ b/var/spack/repos/builtin/packages/vegas2/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 Vegas2(Package): + """"VEGAS2 is an extension that uses 1,000 Genomes data to model SNP + correlations across the autosomes and chromosome X""" + + homepage = "https://vegas2.qimrberghofer.edu.au/" + url = "https://vegas2.qimrberghofer.edu.au/vegas2v2" + + version('2', '815d80b86e9e294f99332bb5181e897a', expand=False) + + depends_on('perl', type='run') + depends_on('r', type='run') + depends_on('plink') + depends_on('r-mvtnorm', type='run') + depends_on('r-corpcor', type='run') + + def url_for_version(self, version): + url = 'https://vegas2.qimrberghofer.edu.au/vegas2v{0}' + return url.format(version) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('vegas2v{0}'.format(self.version), prefix.bin) -- cgit v1.2.3-70-g09d2