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authorTodd Gamblin <tgamblin@llnl.gov>2016-08-07 23:43:40 -0700
committerGitHub <noreply@github.com>2016-08-07 23:43:40 -0700
commitdd30066feb71eef44cd5720d0265ad7aa3c6dc2a (patch)
tree81ea0f1708427dc9872e4f8799fa24a405bf5b48
parente65a8b6a9ae615005119508edb1a93a5f9d80fe4 (diff)
parentf800708ef30f70a8b3f251ca267dee8afc2395d5 (diff)
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Merge pull request #1449 from hartzell/feature/add-package-for-prank
Add package for prank and supporting tools
-rw-r--r--var/spack/repos/builtin/packages/bpp-core/package.py41
-rw-r--r--var/spack/repos/builtin/packages/bpp-phyl/package.py43
-rw-r--r--var/spack/repos/builtin/packages/bpp-seq/package.py42
-rw-r--r--var/spack/repos/builtin/packages/bpp-suite/package.py47
-rw-r--r--var/spack/repos/builtin/packages/exonerate/package.py45
-rw-r--r--var/spack/repos/builtin/packages/mafft/package.py42
-rw-r--r--var/spack/repos/builtin/packages/prank/package.py44
7 files changed, 304 insertions, 0 deletions
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..40360a03b3
--- /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('-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
new file mode 100644
index 0000000000..62db8d5545
--- /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('-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
new file mode 100644
index 0000000000..7132c668b3
--- /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('-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
new file mode 100644
index 0000000000..41e90e375d
--- /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('.', *std_cmake_args)
+ make()
+ make('install')
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..7921e64058
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exonerate/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# 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')
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')
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..d627e8a0b6
--- /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('bpp-suite') # for bppancestor
+
+ def install(self, spec, prefix):
+ with working_dir('src'):
+ make()
+ mkdirp(prefix.bin)
+ install('prank', prefix.bin)