From 5bb86ce9643fdf86c76a1d03499113372ce72e3b Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 9 Aug 2017 21:39:06 -0500 Subject: soapindel: new package (#5048) * soapindel: new package * fixed versioning --- .../repos/builtin/packages/soapindel/package.py | 53 ++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 var/spack/repos/builtin/packages/soapindel/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/soapindel/package.py b/var/spack/repos/builtin/packages/soapindel/package.py new file mode 100644 index 0000000000..6d22660786 --- /dev/null +++ b/var/spack/repos/builtin/packages/soapindel/package.py @@ -0,0 +1,53 @@ +############################################################################## +# 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 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 Soapindel(MakefilePackage): + """SOAPindel is focusing on calling indels from the next-generation + paired-end sequencing data.""" + + homepage = "http://soap.genomics.org.cn/soapindel.html" + + version('2.1.7.17', '317ef494173969cdc6a8244dd87d06bd', + url='http://soap.genomics.org.cn/down/SOAPindel_20130918_2.1.7.17.zip') + + depends_on('perl', type=('build', 'run')) + + build_directory = 'indel_detection.release' + + def install(self, spec, prefix): + with working_dir('indel_detection.release'): + install_tree('tools', prefix.tools) + mkdirp(prefix.lib) + install('affine_align.pm', prefix.lib) + install('indel_lib.pm', prefix.lib) + mkdirp(prefix.bin) + install('assemble_align', prefix.bin) + install('cluster_reads', prefix.bin) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PERL5LIB', self.prefix.lib) + run_env.prepend_path('PATH', self.prefix.tools) -- cgit v1.2.3-70-g09d2