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Add packages for clustalw and clustalo (and argtable) (#4412)

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* Add packages for clustalw and clustalo (and argtable)

Add packages for the classic multiple alignment package, `clustalw`
and its younger sibling, `clustalo`.

`clustalo` needed the `argtable` package (command line arg parsing).

Lightly tested on CentOS 7.

* Remove FIXME (sigh...)
This commit is contained in:
George Hartzell 2017-06-01 10:36:01 -07:00 committed by Adam J. Stewart
parent 916243b23a
commit 391afa9271
3 changed files with 106 additions and 0 deletions
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36
var/spack/repos/builtin/packages/argtable/package.py Normal file
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##############################################################################
# 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 LICENSE file 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 Argtable(AutotoolsPackage):
"""Argtable is an ANSI C library for parsing GNU style command line
options with a minimum of fuss.
"""
homepage = "http://argtable.sourceforge.net/"
url = "https://sourceforge.net/projects/argtable/files/argtable/argtable-2.13/argtable2-13.tar.gz/download"
version('2-13', '156773989d0d6406cea36526d3926668')

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var/spack/repos/builtin/packages/clustalo/package.py Normal file
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##############################################################################
# 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 LICENSE file 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 Clustalo(AutotoolsPackage):
"""Clustal Omega: the last alignment program you'll ever need."""
homepage = "http://www.clustal.org/omega/"
url = "http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz"
version('1.2.4', '6c0459f4c463a30e942ce7e0efc91422')
depends_on('argtable')

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var/spack/repos/builtin/packages/clustalw/package.py Normal file
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##############################################################################
# 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 LICENSE file 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 Clustalw(AutotoolsPackage):
"""Multiple alignment of nucleic acid and protein sequences."""
homepage = "http://www.clustal.org/clustal2/"
url = "http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz"
version('2.1', '144df8440a0ae083d5167616c8ceeb41')