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fastq-screen: new package (#5431)

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* fastq-screen: new package

* fixing descriptions and previously made packages' old copyright date

* added wrong perl package after change
This commit is contained in:
Audrey Thoma 2017-09-28 13:48:31 -05:00 committed by Christoph Junghans
parent 0ce93d7333
commit 3f44eb0179
6 changed files with 228 additions and 0 deletions
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46
var/spack/repos/builtin/packages/fastq-screen/package.py Normal file
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##############################################################################
# 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/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 FastqScreen(Package):
"""FastQ Screen allows you to screen a library of sequences in FastQ format
against a set of sequence databases so you can see if the composition of
the library matches with what you expect."""
homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
url = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz"
version('0.11.2', 'ef79f16ee553aaa0ab2fc14ea11e5473')
depends_on('perl', type='run')
depends_on('perl-gd-graph', type='run')
depends_on('bowtie')
depends_on('bowtie2')
depends_on('bwa')
depends_on('samtools')
def install(self, spec, prefix):
install_tree('.', prefix.bin)

34
var/spack/repos/builtin/packages/perl-capture-tiny/package.py Normal file
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##############################################################################
# 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/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 PerlCaptureTiny(PerlPackage):
"""Capture STDOUT and STDERR from Perl, XS or external programs"""
homepage = "http://search.cpan.org/~dagolden/Capture-Tiny-0.46/lib/Capture/Tiny.pm"
url = "http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.46.tar.gz"
version('0.46', 'd718af07729d26a793949ca6ba2580a7')

34
var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py Normal file
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##############################################################################
# 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/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 PerlExtutilsPkgconfig(PerlPackage):
"""simplistic interface to pkg-config"""
homepage = "http://search.cpan.org/~xaoc/ExtUtils-PkgConfig-1.16/lib/ExtUtils/PkgConfig.pm"
url = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz"
version('1.16', 'b86318f2b6ac6af3ee985299e1e38fe5')

39
var/spack/repos/builtin/packages/perl-gd-graph/package.py Normal file
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##############################################################################
# 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/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 PerlGdGraph(PerlPackage):
"""Graph Plotting Module for Perl 5"""
homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm"
url = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.44.tar.gz"
version('1.4308', 'fcdd34d5e09ae917b5d264887734b3b1')
depends_on('perl-capture-tiny', type=('build', 'run'))
depends_on('perl-test-exception', type=('build', 'run'))
depends_on('perl-gd-text', type=('build', 'run'))
depends_on('perl-gd', type=('build', 'run'))

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var/spack/repos/builtin/packages/perl-gd-text/package.py Normal file
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##############################################################################
# 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/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 PerlGdText(PerlPackage):
"""Text utilities for use with GD"""
homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm"
url = "http://search.cpan.org/CPAN/authors/id/M/MV/MVERB/GDTextUtil-0.86.tar.gz"
version('0.86', '941ad06eadc86b47f3a32da405665c41')
depends_on('perl-gd', type=('build', 'run'))

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var/spack/repos/builtin/packages/perl-gd/package.py Normal file
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##############################################################################
# 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/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 PerlGd(PerlPackage):
"""Interface to Gd Graphics Library"""
homepage = "http://search.cpan.org/~lds/GD-2.53/GD.pm"
url = "http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.53.tar.gz"
version('2.53', 'd2c9b18123bcaff8672eb50f2eb37ed3')
depends_on('perl-module-build', type='build')
depends_on('perl-extutils-makemaker', type=('build', 'run'))
depends_on('perl-extutils-pkgconfig', type=('build', 'run'))
depends_on('libgd')