From 391afa9271f90424917262c48b91b2d9c2a00e2f Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 1 Jun 2017 10:36:01 -0700 Subject: Add packages for clustalw and clustalo (and argtable) (#4412) * Add packages for clustalw and clustalo (and argtable) Add packages for the classic multiple alignment package, `clustalw` and its younger sibling, `clustalo`. `clustalo` needed the `argtable` package (command line arg parsing). Lightly tested on CentOS 7. * Remove FIXME (sigh...) --- .../repos/builtin/packages/argtable/package.py | 36 ++++++++++++++++++++++ .../repos/builtin/packages/clustalo/package.py | 36 ++++++++++++++++++++++ .../repos/builtin/packages/clustalw/package.py | 34 ++++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 var/spack/repos/builtin/packages/argtable/package.py create mode 100644 var/spack/repos/builtin/packages/clustalo/package.py create mode 100644 var/spack/repos/builtin/packages/clustalw/package.py diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py new file mode 100644 index 0000000000..8e1bec15f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/argtable/package.py @@ -0,0 +1,36 @@ +############################################################################## +# 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 Argtable(AutotoolsPackage): + """Argtable is an ANSI C library for parsing GNU style command line + options with a minimum of fuss. + """ + + homepage = "http://argtable.sourceforge.net/" + url = "https://sourceforge.net/projects/argtable/files/argtable/argtable-2.13/argtable2-13.tar.gz/download" + + version('2-13', '156773989d0d6406cea36526d3926668') diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustalo/package.py new file mode 100644 index 0000000000..9e985f0cd7 --- /dev/null +++ b/var/spack/repos/builtin/packages/clustalo/package.py @@ -0,0 +1,36 @@ +############################################################################## +# 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 Clustalo(AutotoolsPackage): + """Clustal Omega: the last alignment program you'll ever need.""" + + homepage = "http://www.clustal.org/omega/" + url = "http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz" + + version('1.2.4', '6c0459f4c463a30e942ce7e0efc91422') + + depends_on('argtable') diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py new file mode 100644 index 0000000000..97f193c628 --- /dev/null +++ b/var/spack/repos/builtin/packages/clustalw/package.py @@ -0,0 +1,34 @@ +############################################################################## +# 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 Clustalw(AutotoolsPackage): + """Multiple alignment of nucleic acid and protein sequences.""" + + homepage = "http://www.clustal.org/clustal2/" + url = "http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz" + + version('2.1', '144df8440a0ae083d5167616c8ceeb41') -- cgit v1.2.3-70-g09d2