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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)
#
# This is a based largely on the Homebrew science formula:
# https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
#
# There s one tricky bit to be resolved:
#
# - HDF5 builds explode, blast's configure script tries to run a program that
# uses a variable called 'HOST' but some other bit defines a macro called
# HOST that's defined to a string. Hilarity ensues.
#
#
from spack import *
class BlastPlus(AutotoolsPackage):
"""Basic Local Alignment Search Tool."""
homepage = "http://blast.ncbi.nlm.nih.gov/"
url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca')
version('2.6.0', 'c8ce8055b10c4d774d995f88c7cc6225')
version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
# homebrew sez: Fixed upstream in future version > 2.6
# But this bug sez that it will be fixed in 2.6
# https://github.com/Homebrew/homebrew-science/pull/4740
# The 2.6.0 src still matches the "before" bit of the patch
# so it's probably still "needed".
# On the other hand, the `find` command is broken and there
# aren't any .svn dirs in the tree, so I've updated their patch
# to just comment out the block.
patch('blast-make-fix2.5.0.diff', when="@2.5.0:2.6.0")
# See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511
@when('@:2.2.31')
def patch(self):
filter_file("2.95* | 2.96* | 3.* | 4.* )",
"2.95* | 2.96* | 3.* | 4.* | 5.* )",
"c++/src/build-system/configure",
string=True)
# No...
# depends_on :mysql => :optional
variant('static', default=False,
description='Build with static linkage')
variant('jpeg', default=True,
description='Build with jpeg support')
variant('png', default=True,
description='Build with png support')
variant('freetype', default=True,
description='Build with freetype support')
# variant('hdf5', default=True,
# description='Build with hdf5 support')
variant('gnutls', default=True,
description='Build with gnutls support')
variant('openssl', default=True,
description='Build with openssl support')
variant('zlib', default=True,
description='Build with zlib support')
variant('bzip2', default=True,
description='Build with bzip2 support')
variant('lzo', default=True,
description='Build with lzo support')
variant('pcre', default=True,
description='Build with pcre support')
variant('perl', default=True,
description='Build with perl support')
variant('python', default=True,
description='Build with python support')
depends_on('jpeg', when='+jpeg')
depends_on('libpng', when='+png')
depends_on('freetype', when='+freetype')
# depends_on('hdf5', when='+hdf5')
depends_on('gnutls', when='+gnutls')
depends_on('openssl', when='+openssl')
depends_on('zlib', when='+zlib')
depends_on('bzip2', when='+bzip2')
depends_on('lzo', when='+lzo')
depends_on('pcre', when='+pcre')
depends_on('python', when='+python')
depends_on('perl', when='+perl')
depends_on('lmdb', when='@2.7.1:')
configure_directory = 'c++'
def configure_args(self):
spec = self.spec
config_args = [
'--with-bin-release',
'--without-debug',
'--with-mt',
'--with-64',
'--without-boost',
]
if '+static' in spec:
config_args.append('--with-static')
# FIXME
# args << "--with-static-exe" unless OS.linux?
# args << "--with-dll" if build.with? "dll"
else:
config_args.extend([
'--with-dll',
'--without-static',
'--without-static-exe'
])
if '+jpeg' in spec:
config_args.append(
'--with-jpeg={0}'.format(self.spec['jpeg'].prefix)
)
else:
config_args.append('--without-jpeg')
if '+png' in spec:
config_args.append(
'--with-png={0}'.format(self.spec['libpng'].prefix)
)
else:
config_args.append('--without-png')
if '+freetype' in spec:
config_args.append(
'--with-freetype={0}'.format(self.spec['freetype'].prefix)
)
else:
config_args.append('--without-freetype')
config_args.append('--without-hdf5')
# if '+hdf5' in spec:
# # FIXME
# config_args.append(
# '--with-hdf5={0}'.format(self.spec['hdf5'].prefix)
# )
# else:
# config_args.append('--without-hdf5')
if '+zlib' in spec:
config_args.append(
'--with-z={0}'.format(self.spec['zlib'].prefix)
)
else:
config_args.append('--without-z')
if '+bzip2' in spec:
config_args.append(
'--with-bz2={0}'.format(self.spec['bzip2'].prefix)
)
else:
config_args.append('--without-bz2')
if '+lzo' in spec:
config_args.append(
'--with-lzo={0}'.format(self.spec['lzo'].prefix)
)
else:
config_args.append('--without-lzo')
if '+gnutls' in spec:
config_args.append(
'--with-gnutls={0}'.format(self.spec['gnutls'].prefix)
)
else:
config_args.append('--without-gnutls')
if '+openssl' in spec:
config_args.append(
'--with-openssl={0}'.format(self.spec['openssl'].prefix)
)
else:
config_args.append('--without-openssl')
if '+pcre' in spec:
config_args.append(
'--with-pcre={0}'.format(self.spec['pcre'].prefix)
)
else:
config_args.append('--without-pcre')
if '+python' in spec:
config_args.append(
'--with-python={0}'.format(self.spec['python'].home)
)
else:
config_args.append('--without-python')
if '+perl' in spec:
config_args.append(
'--with-perl={0}'.format(self.spec['perl'].prefix)
)
else:
config_args.append('--without-python')
return config_args
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