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
2.4 KiB
Python
50 lines
2.4 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 RRsamtools(RPackage):
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"""Binary alignment (BAM), FASTA, variant call (BCF), and tabix file
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import.
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This package provides an interface to the 'samtools', 'bcftools', and
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'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
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FASTA, binary variant call (BCF) and compressed indexed tab-delimited
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(tabix) files."""
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homepage = "https://bioconductor.org/packages/Rsamtools"
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git = "https://git.bioconductor.org/packages/Rsamtools.git"
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version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30')
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version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70')
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version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c')
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version('1.32.3', commit='0aa3f134143b045aa423894de81912becf64e4c2')
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version('1.30.0', commit='61b365fe3762e796b3808cec7238944b7f68d7a6')
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version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472')
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depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
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depends_on('r-genomicranges@1.21.6:', type=('build', 'run'))
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depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
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depends_on('r-biocgenerics@0.1.3:', type=('build', 'run'))
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depends_on('r-s4vectors@0.13.8:', type=('build', 'run'))
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depends_on('r-iranges@2.3.7:', type=('build', 'run'))
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depends_on('r-xvector@0.15.1:', type=('build', 'run'))
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depends_on('r-zlibbioc', type=('build', 'run'))
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depends_on('r-bitops', type=('build', 'run'))
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depends_on('r-biocparallel', type=('build', 'run'))
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depends_on('r-genomicranges@1.31.8:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-biocgenerics@0.25.1:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-s4vectors@0.17.25:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
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depends_on('r-rhtslib@1.16.3', when='@2.0.3', type=('build', 'run'))
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depends_on('r-rhtslib@1.17.7:', when='@2.2.1:', type=('build', 'run'))
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depends_on('gmake', type='build')
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