69 lines
2.4 KiB
Python
69 lines
2.4 KiB
Python
# Copyright 2013-2024 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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import platform
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from spack.package import *
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class Bwa(Package):
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"""Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
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homepage = "https://github.com/lh3/bwa"
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url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
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license("GPL-3.0-only")
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version("0.7.17", sha256="de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd")
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version("0.7.15", sha256="2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515")
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version("0.7.13", sha256="559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc")
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version(
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"0.7.12",
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sha256="285f55b7fa1f9e873eda9a9b06752378a799ecdecbc886bbd9ba238045bf62e0",
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url="https://github.com/lh3/bwa/archive/0.7.12.tar.gz",
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)
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depends_on("zlib-api")
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depends_on("sse2neon", when="target=aarch64:")
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patch(
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"bwa_for_aarch64.patch",
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sha256="b77213b16cf8760f01e32f9a0b2cd8988cf7bac48a11267100f703cbd55c4bfd",
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when="target=aarch64:",
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)
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def install(self, spec, prefix):
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zlib_inc_path = spec["zlib-api"].prefix.include
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if platform.machine() == "aarch64":
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sse2neon_inc_path = spec["sse2neon"].prefix.include
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filter_file(
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r"^INCLUDES=",
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"INCLUDES=-I%s -I%s" % (zlib_inc_path, sse2neon_inc_path),
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"Makefile",
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)
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else:
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filter_file(r"^INCLUDES=", "INCLUDES=-I%s" % zlib_inc_path, "Makefile")
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filter_file(r"^LIBS=", "LIBS=-L%s " % spec["zlib-api"].prefix.lib, "Makefile")
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# use spack C compiler
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filter_file("^CC=.*", "CC={0}".format(spack_cc), "Makefile")
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# fix gcc 10+ errors
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if self.spec.satisfies("%gcc@10:"):
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filter_file(
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"const uint8_t rle_auxtab[8]",
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"extern const uint8_t rle_auxtab[8]",
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"rle.h",
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string=True,
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)
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make()
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mkdirp(prefix.bin)
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install("bwa", join_path(prefix.bin, "bwa"))
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set_executable(join_path(prefix.bin, "bwa"))
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mkdirp(prefix.doc)
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install("README.md", prefix.doc)
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install("NEWS.md", prefix.doc)
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mkdirp(prefix.man.man1)
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install("bwa.1", prefix.man.man1)
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