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Bioawk: added new package (#5375)

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zenln 2017-09-16 02:14:57 -05:00 committed by Massimiliano Culpo
parent fc237792b2
commit 1ce6097651
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var/spack/repos/builtin/packages/bioawk/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 *
from shutil import copyfile
from shutil import copymode
class Bioawk(MakefilePackage):
"""Bioawk is an extension to Brian Kernighan's awk, adding the support of
several common biological data formats, including optionally gzip'ed
BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
"""
homepage = "https://github.com/lh3/bioawk"
url = "https://github.com/lh3/bioawk/archive/v1.0.zip"
version('1.0', 'e423942689f944369de270900978be28')
depends_on('zlib')
depends_on('bison', type=('build'))
parallel = False
def install(self, spec, prefix):
mkdirp(prefix.bin)
copyfile("bioawk", join_path(prefix.bin, "bioawk"))
copymode("bioawk", join_path(prefix.bin, "bioawk"))
copyfile("maketab", join_path(prefix.bin, "maketab"))
copymode("maketab", join_path(prefix.bin, "maketab"))