From e941f33eafe6348e37b6813a284dbe860c2772d1 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Thu, 16 Nov 2017 10:40:46 -0600 Subject: [PATCH] meraculous: new package (#6292) * meraculous: new package * adding gcc version conflict * Update package.py * Update package.py --- .../builtin/packages/meraculous/package.py | 50 +++++++++++++++++++ .../packages/perl-log-log4perl/package.py | 34 +++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 var/spack/repos/builtin/packages/meraculous/package.py create mode 100644 var/spack/repos/builtin/packages/perl-log-log4perl/package.py diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py new file mode 100644 index 0000000000..51d3943943 --- /dev/null +++ b/var/spack/repos/builtin/packages/meraculous/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 Meraculous(CMakePackage): + """Meraculous is a while genome assembler for Next Generation Sequencing + data geared for large genomes.""" + + homepage = "http://jgi.doe.gov/data-and-tools/meraculous/" + url = "https://downloads.sourceforge.net/project/meraculous20/Meraculous-v2.2.4.tar.gz" + + version('2.2.4', '349feb6cb178643a46e4b092c87bad3a') + + depends_on('perl', type=('build', 'run')) + depends_on('boost@1.5.0:') + depends_on('gnuplot@3.7:') + depends_on('perl-log-log4perl', type=('build', 'run')) + + conflicts('%gcc@6.0.0:', when='@2.2.4') + + def patch(self): + edit = FileFilter('CMakeLists.txt') + edit.filter("-static-libstdc\+\+", "") + + def setup_environment(self, spack_env, run_env): + run_env.set('MERACULOUS_ROOT', self.prefix) + run_env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py new file mode 100644 index 0000000000..6a0d182d2f --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py @@ -0,0 +1,34 @@ +############################################################################## +# 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 PerlLogLog4perl(PerlPackage): + """Log4j implementation for Perl""" + + homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm" + url = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz" + + version('146', '500abbd978ed326cfe5367dc4f9f3be2')