779e80b7c1
* cleaned up style, linked to external htslib * removed htslib/bcfrools/samtools deps, use bundled libs instead the pysam package includes the necessary libs to link to, so it wasn't even using linked libs when building * fixed style * revert to using external htslib currently uses bundled samtools and bcftools, and there is no way to use external versions for those dependencies * added libs property to htslibs package added support for lib64 * added htslib name
44 lines
2.1 KiB
Python
44 lines
2.1 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 PyPysam(PythonPackage):
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"""A python module for reading, manipulating and writing genomic data
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sets."""
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homepage = "https://github.com/pysam-developers/pysam"
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pypi = "pysam/pysam-0.14.1.tar.gz"
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version("0.19.1", sha256="dee403cbdf232170c1e11cc24c76e7dd748fc672ad38eb0414f3b9d569b1448f")
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version("0.18.0", sha256="1d6d49a0b3c626fae410a93d4c80583a8b5ddaacc9b46a080b250dbcebd30a59")
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version("0.15.3", sha256="a98dd0a164aa664b1ab30a36f653752f00e93c13deeb66868597f4b2a30f7265")
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version("0.15.2", sha256="d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9")
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version("0.15.1", sha256="658421124c2f3de1b7445e03ca8413df0077f67ea9980abdaab0d1b5f7a8936f")
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version("0.14.1", sha256="2e86f5228429d08975c8adb9030296699012a8deba8ba26cbfc09b374f792c97")
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version("0.7.7", sha256="c9f3018482eec99ee199dda3fdef2aa7424dde6574672a4c0d209a10985755cc")
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depends_on("py-setuptools", type="build")
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depends_on("py-cython@0.29.12:", when="@0.18:", type="build")
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depends_on("py-cython@0.21:", when="@0.14:", type="build")
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depends_on("py-cython@0.17:", type="build")
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depends_on("curl")
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depends_on("xz")
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depends_on("htslib@:1.6", when="@:0.13")
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depends_on("htslib")
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def setup_build_environment(self, env):
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env.set("LDFLAGS", self.spec["curl"].libs.search_flags)
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# this flag is supposed to be removed by cy_build.py, but for some reason isn't
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if self.spec.platform == "darwin":
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env.remove_flags("LDSHARED", "-bundle")
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# linking htslib, see:
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# http://pysam.readthedocs.org/en/latest/installation.html#external
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# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
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env.set("HTSLIB_MODE", "external")
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env.set("HTSLIB_LIBRARY_DIR", self.spec["htslib"].libs.directories[0])
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env.set("HTSLIB_INCLUDE_DIR", self.spec["htslib"].headers.directories[0])
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