cleaveland4: new package (#4894)
* cleaveland4: new package * fixing return line in viennarna url_for_version
This commit is contained in:
Audrey Thoma
Adam J. Stewart
parent
20ab66a2e9
commit
71991cd9c9
48
var/spack/repos/builtin/packages/cleaveland4/package.py
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48
var/spack/repos/builtin/packages/cleaveland4/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Cleaveland4(Package):
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"""CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA
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targets"""
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homepage = "https://github.com/MikeAxtell/CleaveLand4"
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url = "https://github.com/MikeAxtell/CleaveLand4/archive/v4.4.tar.gz"
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version('4.4', 'cf62a1de715a612fc8bd5a62364e69db')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-math-cdf', type=('build', 'run'))
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depends_on('bowtie')
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depends_on('viennarna')
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depends_on('r', type=('build', 'run'))
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depends_on('samtools')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('CleaveLand4.pl', prefix.bin)
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with working_dir('GSTAr_v1-0'):
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install('GSTAr.pl', prefix.bin)
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35
var/spack/repos/builtin/packages/perl-math-cdf/package.py
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35
var/spack/repos/builtin/packages/perl-math-cdf/package.py
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@ -0,0 +1,35 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PerlMathCdf(PerlPackage):
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"""Generate probabilities and quantiles from several statistical
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probability functions"""
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homepage = "http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm"
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url = "http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz"
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version('0.1', '7866c7b6b9d27f0ce4b7637334478ab7')
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67
var/spack/repos/builtin/packages/viennarna/package.py
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67
var/spack/repos/builtin/packages/viennarna/package.py
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@ -0,0 +1,67 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Viennarna(AutotoolsPackage):
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"""The ViennaRNA Package consists of a C code library and several
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stand-alone programs for the prediction and comparison of RNA secondary
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structures."""
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homepage = "https://www.tbi.univie.ac.at/RNA/"
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url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz"
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version('2.3.5', '4542120adae9b7abb605e2304c2a1326')
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variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
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variant('perl', default=True, description='Build ViennaRNA with Perl interface')
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variant('python', default=True, description='Build ViennaRNA with Python interface')
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depends_on('perl', type=('build', 'run'))
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depends_on('python', type=('build', 'run'))
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depends_on('libsvm')
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depends_on('gsl')
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def url_for_version(self, version):
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url = 'https://www.tbi.univie.ac.at/RNA/download/sourcecode/{0}_x/ViennaRNA-{1}.tar.gz'
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return url.format(version.up_to(2).underscored, version)
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def configure_args(self):
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args = []
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if '+sse' in self.spec:
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args.append('--enable-sse')
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else:
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args.append('--disable-sse')
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if '~python' in self.spec:
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args.append('--without-python')
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else:
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args.append('--with-python')
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if '~perl' in self.spec:
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args.append('--without-perl')
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else:
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args.append('--with-perl')
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if 'python@3:' in self.spec:
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args.append('--with-python3')
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return args
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