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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import platform
from spack.package import *
class Bwa(Package):
"""Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
homepage = "https://github.com/lh3/bwa"
url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
license("GPL-3.0-only")
version("0.7.17", sha256="de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd")
version("0.7.15", sha256="2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515")
version("0.7.13", sha256="559b3c63266e5d5351f7665268263dbb9592f3c1c4569e7a4a75a15f17f0aedc")
version(
"0.7.12",
sha256="285f55b7fa1f9e873eda9a9b06752378a799ecdecbc886bbd9ba238045bf62e0",
url="https://github.com/lh3/bwa/archive/0.7.12.tar.gz",
)
depends_on("zlib-api")
depends_on("sse2neon", when="target=aarch64:")
patch(
"bwa_for_aarch64.patch",
sha256="b77213b16cf8760f01e32f9a0b2cd8988cf7bac48a11267100f703cbd55c4bfd",
when="target=aarch64:",
)
def install(self, spec, prefix):
zlib_inc_path = spec["zlib-api"].prefix.include
if platform.machine() == "aarch64":
sse2neon_inc_path = spec["sse2neon"].prefix.include
filter_file(
r"^INCLUDES=",
"INCLUDES=-I%s -I%s" % (zlib_inc_path, sse2neon_inc_path),
"Makefile",
)
else:
filter_file(r"^INCLUDES=", "INCLUDES=-I%s" % zlib_inc_path, "Makefile")
filter_file(r"^LIBS=", "LIBS=-L%s " % spec["zlib-api"].prefix.lib, "Makefile")
# use spack C compiler
filter_file("^CC=.*", "CC={0}".format(spack_cc), "Makefile")
# fix gcc 10+ errors
if self.spec.satisfies("%gcc@10:"):
filter_file(
"const uint8_t rle_auxtab[8]",
"extern const uint8_t rle_auxtab[8]",
"rle.h",
string=True,
)
make()
mkdirp(prefix.bin)
install("bwa", join_path(prefix.bin, "bwa"))
set_executable(join_path(prefix.bin, "bwa"))
mkdirp(prefix.doc)
install("README.md", prefix.doc)
install("NEWS.md", prefix.doc)
mkdirp(prefix.man.man1)
install("bwa.1", prefix.man.man1)
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