From 1ce60976513d7caddf26733bc26ed1f513586d00 Mon Sep 17 00:00:00 2001 From: zenln Date: Sat, 16 Sep 2017 02:14:57 -0500 Subject: Bioawk: added new package (#5375) --- var/spack/repos/builtin/packages/bioawk/package.py | 51 ++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bioawk/package.py diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py new file mode 100644 index 0000000000..80d90c7149 --- /dev/null +++ b/var/spack/repos/builtin/packages/bioawk/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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/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")) -- cgit v1.2.3-70-g09d2