725336ee48
This PR adds an updated version to the r-rhtslib package as well as fix the build. - add patches to use compiler flags from R - add variables for bzip2 and xz dependencies - use the spack Makeconf file when building the in-tree htslib - make patchelf available to allow R to remove reference to temporary installation directory in htslib shared object - Add new version of r-rsamtools as the r-rsamtools and r-rhtlib packages are closely paired.
50 lines
2.1 KiB
Python
50 lines
2.1 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class RRhtslib(RPackage):
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"""HTSlib high-throughput sequencing library as an R package.
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This package provides version 1.7 of the 'HTSlib' C library for high-
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throughput sequence analysis. The package is primarily useful to
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developers of other R packages who wish to make use of HTSlib.
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Motivation and instructions for use of this package are in the vignette,
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vignette(package="Rhtslib", "Rhtslib")."""
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homepage = "https://bioconductor.org/packages/Rhtslib"
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git = "https://git.bioconductor.org/packages/Rhtslib.git"
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version('1.18.1', commit='751a2ebaed43b7991204b27bd6c7870645001d82')
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version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4')
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version('1.14.1', commit='4be260720f845a34d0ac838278fce1363f645230')
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version('1.12.1', commit='e3487b1355995d09b28fde5d0a7504a3e79a7203')
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version('1.10.0', commit='53dcf7dfe35d735283956c77c011a97ca3f4eb26')
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version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79')
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depends_on('r-zlibbioc', type=('build', 'run'))
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depends_on('bzip2', type=('build', 'link', 'run'))
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depends_on('xz', type=('build', 'link', 'run'))
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depends_on('curl', type=('build', 'link', 'run'))
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depends_on('gmake', type='build')
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# Some versions of this package will leave the temporary installation
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# directory in the htslib shared object. R will fix this if patchelf is
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# available
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depends_on('patchelf', when='@1.12:1.14', type='build')
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patch('use_spack_Makeconf.patch', when='@1.12:')
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patch('find_deps-1.12.patch', when='@1.12:1.14')
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patch('find_deps-1.16.patch', when='@1.16:')
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@when('@1.12:')
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def setup_build_environment(self, env):
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env.set('BZIP2_INCLUDE', self.spec['bzip2'].headers.include_flags)
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env.set('XZ_INCLUDE', self.spec['xz'].headers.include_flags)
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env.set('BZIP2_LIB', self.spec['bzip2'].libs.search_flags)
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env.set('XZ_LIB', self.spec['xz'].libs.search_flags)
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