1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
|
##############################################################################
# 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/spack/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"))
|
