From a07a0ef54b43089eb608c0b464db2e2f5f79c115 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 26 Jul 2016 17:18:37 -0400 Subject: Add Bio++ tool suite and supporting libs Add the Bio++ suite and its supporting libraries. --- .../repos/builtin/packages/bpp-core/package.py | 41 +++++++++++++++++++ .../repos/builtin/packages/bpp-phyl/package.py | 43 ++++++++++++++++++++ .../repos/builtin/packages/bpp-seq/package.py | 42 +++++++++++++++++++ .../repos/builtin/packages/bpp-suite/package.py | 47 ++++++++++++++++++++++ 4 files changed, 173 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bpp-core/package.py create mode 100644 var/spack/repos/builtin/packages/bpp-phyl/package.py create mode 100644 var/spack/repos/builtin/packages/bpp-seq/package.py create mode 100644 var/spack/repos/builtin/packages/bpp-suite/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py new file mode 100644 index 0000000000..0a10914726 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 LICENSE file 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 BppCore(Package): + """Bio++ core library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz" + + version('2.2.0', '5789ed2ae8687d13664140cd77203477') + + depends_on('cmake') + + def install(self, spec, prefix): + cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py new file mode 100644 index 0000000000..2240f7bd2f --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 LICENSE file 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 BppPhyl(Package): + """Bio++ phylogeny library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz" + + version('2.2.0', '5c40667ec0bf37e0ecaba321be932770') + + depends_on('cmake') + depends_on('bpp-core') + depends_on('bpp-seq') + + def install(self, spec, prefix): + cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py new file mode 100644 index 0000000000..398fda528e --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 LICENSE file 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 BppSeq(Package): + """Bio++ seq library.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" + url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz" + + version('2.2.0', '44adef0ff4d5ca4e69ccf258c9270633') + + depends_on('cmake') + depends_on('bpp-core') + + def install(self, spec, prefix): + cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py new file mode 100644 index 0000000000..872c72d498 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 LICENSE file 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 BppSuite(Package): + """BppSuite is a suite of ready-to-use programs for phylogenetic and + sequence analysis.""" + + homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite" + url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz" + + version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4') + + # FIXME: Add dependencies if required. + depends_on('cmake') + depends_on('texinfo') + depends_on('bpp-core') + depends_on('bpp-seq') + depends_on('bpp-phyl') + + def install(self, spec, prefix): + cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '.') + make() + make('install') -- cgit v1.2.3-60-g2f50