From 63592096c5ec7ddf4072512303b96ad1505d5659 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 26 Jul 2016 17:25:40 -0400 Subject: Add package for prank --- var/spack/repos/builtin/packages/prank/package.py | 44 +++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/prank/package.py diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py new file mode 100644 index 0000000000..f551da3966 --- /dev/null +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 Prank(Package): + """A powerful multiple sequence alignment browser.""" + + homepage = "http://wasabiapp.org/software/prank/" + url = "http://wasabiapp.org/download/prank/prank.source.140603.tgz" + + version('150803', '71ac2659e91c385c96473712c0a23e8a') + + depends_on('mafft') + depends_on('exonerate') + depends_on('bppsuite') # for bppancestor + + def install(self, spec, prefix): + with working_dir('src'): + make() + mkdirp(prefix.bin) + install('prank', prefix.bin) -- cgit v1.2.3-60-g2f50 From 9e16902397245cf2dd448710362ac003f2a2711d Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 28 Jul 2016 19:48:17 -0400 Subject: Fix name of bpp-suite (missing -...) --- var/spack/repos/builtin/packages/prank/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index f551da3966..d627e8a0b6 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -35,7 +35,7 @@ class Prank(Package): depends_on('mafft') depends_on('exonerate') - depends_on('bppsuite') # for bppancestor + depends_on('bpp-suite') # for bppancestor def install(self, spec, prefix): with working_dir('src'): -- cgit v1.2.3-60-g2f50 From e0db1f0268c192350fe38baac85620a504b2ce70 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 26 Jul 2016 17:22:44 -0400 Subject: Add package for exonerate --- .../repos/builtin/packages/exonerate/package.py | 44 ++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/exonerate/package.py diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py new file mode 100644 index 0000000000..dcc20af2f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/exonerate/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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 Exonerate(Package): + """Pairwise sequence alignment of DNA and proteins""" + + homepage = "http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" + url = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz" + + version('2.4.0', '126fbade003b80b663a1d530c56f1904') + + depends_on('pkg-config', type="build") + depends_on('glib') + + parallel = False + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix), '--disable-debug', '--disable-dependency-tracking') + make() + make('install') -- cgit v1.2.3-60-g2f50 From 3c81bb44baab2e3c7d038a61545fcd880a3f261a Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 26 Jul 2016 17:23:56 -0400 Subject: Add package for mafft --- var/spack/repos/builtin/packages/mafft/package.py | 42 +++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mafft/package.py diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py new file mode 100644 index 0000000000..131b8c58f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/mafft/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 Mafft(Package): + """MAFFT is a multiple sequence alignment program for unix-like + operating systems. It offers a range of multiple alignment + methods, L-INS-i (accurate; for alignment of <~200 sequences), + FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.""" + + homepage = "http://mafft.cbrc.jp/alignment/software/index.html" + url = "http://mafft.cbrc.jp/alignment/software/mafft-7.221-with-extensions-src.tgz" + + version('7.221', 'b1aad911e51024d631722a2e061ba215') + + def install(self, spec, prefix): + with working_dir('core'): + make('PREFIX=%s' % prefix) + make('PREFIX=%s' % prefix, 'install') -- cgit v1.2.3-60-g2f50 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 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 From 6a62a6b693f020bb221902c9049afdb947492708 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 4 Aug 2016 15:10:45 -0400 Subject: Flake8 whitespace cleanup --- var/spack/repos/builtin/packages/bpp-core/package.py | 3 ++- var/spack/repos/builtin/packages/bpp-phyl/package.py | 3 ++- var/spack/repos/builtin/packages/bpp-seq/package.py | 3 ++- var/spack/repos/builtin/packages/exonerate/package.py | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index 0a10914726..987fd964b9 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -36,6 +36,7 @@ class BppCore(Package): depends_on('cmake') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + 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 index 2240f7bd2f..c50f71385a 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -38,6 +38,7 @@ class BppPhyl(Package): depends_on('bpp-seq') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + 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 index 398fda528e..dff26b3308 100644 --- a/var/spack/repos/builtin/packages/bpp-seq/package.py +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -37,6 +37,7 @@ class BppSeq(Package): depends_on('bpp-core') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '-DBUILD_TESTING=FALSE', '.') + cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, + '-DBUILD_TESTING=FALSE', '.') make() make('install') diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py index dcc20af2f9..7921e64058 100644 --- a/var/spack/repos/builtin/packages/exonerate/package.py +++ b/var/spack/repos/builtin/packages/exonerate/package.py @@ -39,6 +39,7 @@ class Exonerate(Package): parallel = False def install(self, spec, prefix): - configure('--prefix={0}'.format(prefix), '--disable-debug', '--disable-dependency-tracking') + configure('--prefix={0}'.format(prefix), '--disable-debug', + '--disable-dependency-tracking') make() make('install') -- cgit v1.2.3-60-g2f50 From f800708ef30f70a8b3f251ca267dee8afc2395d5 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Fri, 5 Aug 2016 18:11:05 -0400 Subject: Switch to using *std_cmake_args --- var/spack/repos/builtin/packages/bpp-core/package.py | 3 +-- var/spack/repos/builtin/packages/bpp-phyl/package.py | 3 +-- var/spack/repos/builtin/packages/bpp-seq/package.py | 3 +-- var/spack/repos/builtin/packages/bpp-suite/package.py | 2 +- 4 files changed, 4 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index 987fd964b9..40360a03b3 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -36,7 +36,6 @@ class BppCore(Package): depends_on('cmake') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DBUILD_TESTING=FALSE', '.') + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) 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 index c50f71385a..62db8d5545 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -38,7 +38,6 @@ class BppPhyl(Package): depends_on('bpp-seq') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DBUILD_TESTING=FALSE', '.') + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) 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 index dff26b3308..7132c668b3 100644 --- a/var/spack/repos/builtin/packages/bpp-seq/package.py +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -37,7 +37,6 @@ class BppSeq(Package): depends_on('bpp-core') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, - '-DBUILD_TESTING=FALSE', '.') + cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args) 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 index 872c72d498..41e90e375d 100644 --- a/var/spack/repos/builtin/packages/bpp-suite/package.py +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -42,6 +42,6 @@ class BppSuite(Package): depends_on('bpp-phyl') def install(self, spec, prefix): - cmake('-DCMAKE_INSTALL_PREFIX=%s' % prefix, '.') + cmake('.', *std_cmake_args) make() make('install') -- cgit v1.2.3-60-g2f50