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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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/hmmer/hmmer-3.2.1.tar.gz'
version('3.2.1', '4e0ad5ed45462d4e36807d21e6d82b69')
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 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')
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