43 lines
1.9 KiB
Python
43 lines
1.9 KiB
Python
# Copyright 2013-2023 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.package import *
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class RBamsignals(RPackage):
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"""Extract read count signals from bam files.
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This package allows to efficiently obtain count vectors from indexed bam
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files. It counts the number of reads in given genomic ranges and it
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computes reads profiles and coverage profiles. It also handles paired-
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end data."""
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bioc = "bamsignals"
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version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe")
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version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917")
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version("1.26.0", commit="d57643441d04f77db0907637dc9e7cd5bed5842f")
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version("1.22.0", commit="5f533969c84212406bcb3ebf725ebb6d77e9947a")
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version("1.16.0", commit="dba9a4ae1613d2700f122ade1e9b90ca8fce5657")
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version("1.14.0", commit="3107d3a35830e879eeddf127a81016ea1ca9b53d")
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version("1.12.1", commit="06b6282df377cf9db58e8016be4ac8ddcc960939")
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version("1.10.0", commit="7499312ce71e8680680eda10b49d7dff682fc776")
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version("1.8.0", commit="b123b83e8e026c9ec91209d4498aff3e95a5de23")
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depends_on("r@3.2.0:", type=("build", "run"))
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depends_on("r@3.5.0:", type=("build", "run"), when="@1.28.0:")
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depends_on("r-biocgenerics", type=("build", "run"))
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depends_on("r-rcpp@0.10.6:", type=("build", "run"))
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depends_on("r-iranges", type=("build", "run"))
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depends_on("r-genomicranges", type=("build", "run"))
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depends_on("r-zlibbioc", type=("build", "run"))
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depends_on("r-rhtslib", type=("build", "run"))
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depends_on("r-rhtslib@1.12.1:", type=("build", "run"), when="@1.12.1:")
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depends_on("r-rhtslib@1.13.1:", type=("build", "run"), when="@1.14.0:")
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depends_on("gmake", type="build")
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# this is not listed but is needed
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depends_on("curl")
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