From a0df5ae3e08af516a94b0bb4652289c18c36adb1 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 21 Nov 2017 16:58:20 -0600 Subject: phantompeakqualtools: new package (#6403) --- .../packages/phantompeakqualtools/package.py | 44 +++++++++++++++++++ .../packages/r-phantompeakqualtools/package.py | 49 ++++++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 var/spack/repos/builtin/packages/phantompeakqualtools/package.py create mode 100644 var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py new file mode 100644 index 0000000000..6e82b9ec9e --- /dev/null +++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 Phantompeakqualtools(RPackage): + """This package computes informative enrichment and quality measures for + ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.""" + + homepage = "https://github.com/kundajelab/phantompeakqualtools" + url = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz" + + version('1.2', 'e94943a42132b9ff2886f006ab34c121') + + depends_on('awk') + depends_on('samtools') + depends_on('r', type=('build', 'run')) + depends_on('r-phantompeakqualtools', type=('build', 'run')) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('run_spp.R', prefix.bin) diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py new file mode 100644 index 0000000000..d32f402974 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 RPhantompeakqualtools(RPackage): + """Computes informative enrichment and quality measures for + ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version + of r-spp to be used in conjunction with the phantompeakqualtools + package.""" + + homepage = "https://github.com/kundajelab/phantompeakqualtools" + url = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz" + + version('1.14', '4de207d570999170c1bf45bcba8c6d2d') + + depends_on('boost@1.41.0:') + depends_on('r-catools', type=('build', 'run')) + depends_on('r-snow', type=('build', 'run')) + depends_on('r-snowfall', type=('build', 'run')) + depends_on('r-bitops', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + + conflicts('%gcc@6:') + + def setup_environment(self, spack_env, run_env): + spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) -- cgit v1.2.3-60-g2f50