From 71991cd9c9c046e69ee4bcc478b2925dd4ded774 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 25 Jul 2017 13:18:34 -0500 Subject: cleaveland4: new package (#4894) * cleaveland4: new package * fixing return line in viennarna url_for_version --- .../repos/builtin/packages/cleaveland4/package.py | 48 ++++++++++++++++ .../builtin/packages/perl-math-cdf/package.py | 35 +++++++++++ .../repos/builtin/packages/viennarna/package.py | 67 ++++++++++++++++++++++ 3 files changed, 150 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cleaveland4/package.py create mode 100644 var/spack/repos/builtin/packages/perl-math-cdf/package.py create mode 100644 var/spack/repos/builtin/packages/viennarna/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py new file mode 100644 index 0000000000..505f800ac7 --- /dev/null +++ b/var/spack/repos/builtin/packages/cleaveland4/package.py @@ -0,0 +1,48 @@ +############################################################################## +# 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 Cleaveland4(Package): + """CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA + targets""" + + homepage = "https://github.com/MikeAxtell/CleaveLand4" + url = "https://github.com/MikeAxtell/CleaveLand4/archive/v4.4.tar.gz" + + version('4.4', 'cf62a1de715a612fc8bd5a62364e69db') + + depends_on('perl', type=('build', 'run')) + depends_on('perl-math-cdf', type=('build', 'run')) + depends_on('bowtie') + depends_on('viennarna') + depends_on('r', type=('build', 'run')) + depends_on('samtools') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('CleaveLand4.pl', prefix.bin) + with working_dir('GSTAr_v1-0'): + install('GSTAr.pl', prefix.bin) diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py new file mode 100644 index 0000000000..6d7d195dea --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py @@ -0,0 +1,35 @@ +############################################################################## +# 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 PerlMathCdf(PerlPackage): + """Generate probabilities and quantiles from several statistical + probability functions""" + + homepage = "http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm" + url = "http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz" + + version('0.1', '7866c7b6b9d27f0ce4b7637334478ab7') diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py new file mode 100644 index 0000000000..548aacb56f --- /dev/null +++ b/var/spack/repos/builtin/packages/viennarna/package.py @@ -0,0 +1,67 @@ +############################################################################## +# 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 Viennarna(AutotoolsPackage): + """The ViennaRNA Package consists of a C code library and several + stand-alone programs for the prediction and comparison of RNA secondary + structures.""" + + homepage = "https://www.tbi.univie.ac.at/RNA/" + url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz" + + version('2.3.5', '4542120adae9b7abb605e2304c2a1326') + + variant('sse', default=True, description='Enable SSE in order to substantially speed up execution') + variant('perl', default=True, description='Build ViennaRNA with Perl interface') + variant('python', default=True, description='Build ViennaRNA with Python interface') + + depends_on('perl', type=('build', 'run')) + depends_on('python', type=('build', 'run')) + depends_on('libsvm') + depends_on('gsl') + + def url_for_version(self, version): + url = 'https://www.tbi.univie.ac.at/RNA/download/sourcecode/{0}_x/ViennaRNA-{1}.tar.gz' + return url.format(version.up_to(2).underscored, version) + + def configure_args(self): + args = [] + if '+sse' in self.spec: + args.append('--enable-sse') + else: + args.append('--disable-sse') + if '~python' in self.spec: + args.append('--without-python') + else: + args.append('--with-python') + if '~perl' in self.spec: + args.append('--without-perl') + else: + args.append('--with-perl') + if 'python@3:' in self.spec: + args.append('--with-python3') + return args -- cgit v1.2.3-70-g09d2