From e3c708fafedb9313eb4d34fec1e271ffb290de06 Mon Sep 17 00:00:00 2001 From: Eric Date: Mon, 23 Apr 2018 16:11:27 -0500 Subject: [PATCH] prinseq-lite: Create new package (#7873) * prinseq-lite: Create new package * prinseq-lite: set variant description and add dependency type --- .../builtin/packages/prinseq-lite/package.py | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 var/spack/repos/builtin/packages/prinseq-lite/package.py diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py new file mode 100644 index 0000000000..164044ec96 --- /dev/null +++ b/var/spack/repos/builtin/packages/prinseq-lite/package.py @@ -0,0 +1,60 @@ +############################################################################## +# 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 * + + +class PrinseqLite(Package): + """PRINSEQ will help you to preprocess your genomic or metagenomic + sequence data in FASTA or FASTQ format.""" + + homepage = "http://prinseq.sourceforge.net" + url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz" + + version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5') + + variant('nopca', default=True, description="Graphs version without PCA") + + depends_on('perl', type='run') + depends_on('perl-cairo', type='run') + depends_on('perl-digest-md5', type='run') + depends_on('perl-json', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', + 'prinseq-graphs-noPCA.pl') + + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', + 'prinseq-lite.pl') + + install('prinseq-graphs-noPCA.pl', prefix.bin) + install('prinseq-lite.pl', prefix.bin) + + chmod = which('chmod') + chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl')) + chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))