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# Copyright 2013-2021 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)
class Salmon(CMakePackage):
"""Salmon is a tool for quantifying the expression of transcripts using
RNA-seq data."""
homepage = "http://combine-lab.github.io/salmon/"
url = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
version('1.4.0', sha256='6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d')
version('0.14.1', sha256='05289170e69b5f291a8403b40d6b9bff54cc38825e9f721c210192b51a19273e')
version('0.12.0', sha256='91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3')
version('0.9.1', sha256='3a32c28d217f8f0af411c77c04144b1fa4e6fd3c2f676661cc875123e4f53520')
version('0.8.2', sha256='299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91')
variant('build_type', default='RELEASE',
description='CMake build type',
values=('DEBUG', 'RELEASE'))
depends_on('tbb')
depends_on('boost@:1.66.0', when='@:0.14.1')
depends_on('boost@1.72.0:', when='@1.4.0:')
depends_on('cereal')
depends_on('jemalloc')
depends_on('xz')
depends_on('zlib')
depends_on('bzip2')
depends_on('libdivsufsort')
depends_on('staden-io-lib~curl')
depends_on('libgff')
depends_on('pkgconfig')
depends_on('curl', when='@0.14.1:')
conflicts('%gcc@:5.1', when='@0.14.1:')
resources = [
('1.4.0', 'pufferfish', '059207e8d3134060ed70595e53f4189954c9e5edfaa6361b46304f55d1b71bc7'),
('0.14.1', 'RapMap', 'fabac2f360513b803aa3567415eddcd97261ab8a23d4f600af5f98ee8ffd944b'),
('0.12.0', 'RapMap', '05102c0bbc8a0c0056a01cd0e8788fa5b504aee58ac226ab8c0e3ffec8019790'),
('0.9.1', 'RapMap', '8975e5a1ed61ed9354ba776272927545f417ecdce95823e71ba1e7b61de7d380'),
('0.8.2', 'RapMap', '1691f4bca2b604f05f36772ae45faf0842ab4809843df770bd10366a5cfd6822'),
]
for ver, repo, checksum in resources:
resource(name='rapmap',
url='https://github.com/COMBINE-lab/{0}/archive/salmon-v{1}.zip'.format(repo, ver),
sha256=checksum,
placement='external',
expand=False,
when='@{0}'.format(ver))
def patch(self):
# remove static linking to libstdc++
filter_file('-static-libstdc++', '', 'CMakeLists.txt', string=True)
if self.spec.satisfies('@0.8.2:0.9.1'):
filter_file('${FAST_MALLOC_LIB}',
'${FAST_MALLOC_LIB}\n'
'${CMAKE_DL_LIBS}',
'src/CMakeLists.txt',
string=True)
if self.spec.satisfies('@:0.14.1'):
filter_file('curl -k.*',
'',
'scripts/fetchRapMap.sh')
symlink('./salmon-v{0}.zip'.format(self.version),
'./external/rapmap.zip')
if self.spec.satisfies('@1.4.0:'):
filter_file('curl -k.*',
'',
'scripts/fetchPufferfish.sh')
symlink('./salmon-v{0}.zip'.format(self.version),
'./external/pufferfish.zip')
# Fix issues related to lto-wrapper during install
filter_file('INTERPROCEDURAL_OPTIMIZATION True',
'INTERPROCEDURAL_OPTIMIZATION False',
'src/CMakeLists.txt', string=True)
filter_file('curl -k.*', '', 'scripts/fetchPufferfish.sh')
def cmake_args(self):
args = [
'-DBOOST_ROOT=%s' % self.spec['boost'].prefix,
]
return args
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