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authorMitchell Devlin <devlin@blogin4.lcrc.anl.gov>2016-07-14 14:22:23 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2016-07-15 11:03:57 -0500
commit5f1b6f000daef95f4797dde7c419e21439243c9b (patch)
tree2d8c718b9ffedd8a9af48ea4e1ccc311c7e8e6b6 /var
parentd24c11f2b10a180316168f2078f9ba1bfeb5bb23 (diff)
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add HMMER package
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/hmmer/package.py76
1 files changed, 76 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py
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+++ b/var/spack/repos/builtin/packages/hmmer/package.py
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+##############################################################################
+# 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 Hmmer(Package):
+ """HMMER is used for searching sequence databases for sequence homologs,
+ and for making sequence alignments. It implements methods using
+ probabilistic models called profile hidden Markov models (profile HMMs).
+ """
+ homepage = 'http://www.hmmer.org'
+ url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+
+ version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
+ version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588')
+ version('2.4i', 'dab234c87e026ac1de942450750acd20')
+ version('2.3.2', '5f073340c0cf761288f961a73821228a')
+ version('2.3.1', 'c724413e5761c630892506698a4716e2')
+
+ variant('mpi', default=True, description='Compile with MPI')
+ variant('gsl', default=False, description='Compile with GSL')
+
+ depends_on('mpi', when='+mpi')
+ depends_on('gsl', when='+gsl')
+
+ def url_for_version(self, version):
+ base_url = 'http://eddylab.org/software'
+
+ if version >= Version('3.0'):
+ return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+ else:
+ return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+
+ def install(self, spec, prefix):
+ configure_args = [
+ '--prefix={0}'.format(prefix)
+ ]
+
+ if '+gsl' in self.spec:
+ configure_args.extend([
+ '--with-gsl',
+ 'LIBS=-lgsl -lgslcblas'
+ ])
+
+ if '+mpi' in self.spec:
+ configure_args.append('--enable-mpi')
+
+ configure(*configure_args)
+ make()
+
+ if self.run_tests:
+ make('check')
+
+ make('install')