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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)
from glob import glob
from spack.package import *
class NcbiToolkit(AutotoolsPackage):
"""NCBI C++ Toolkit"""
homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--22_0_0.tar.gz"
# Per https://ncbi.github.io/cxx-toolkit/pages/ch_getcode_svn#ch_getcode_svn.external
# New versions are released on github
version(
"26_0_1",
sha256="aba79da5c8d0407ffc92b7831f4f8f8a8096a15e47a016ada81b6568f9d280cc",
url="https://github.com/ncbi/ncbi-cxx-toolkit-public/archive/refs/tags/release-26.0.1.tar.gz",
)
version(
"25_2_0",
sha256="9f824a92750e64e7b9be98d82b84414ab4f7e5d73392dadbb87c94ff5ccf9111",
url="https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--25_2_0.tar.gz",
)
version(
"22_0_0",
sha256="ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f",
url="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/Mar_28_2019/ncbi_cxx--22_0_0.tar.gz",
)
version(
"21_0_0",
sha256="48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f",
url="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2018/Apr_2_2018/ncbi_cxx--21_0_0.tar.gz",
)
variant("debug", default=False, description="Build debug versions of libs and apps")
depends_on("boost@1.35.0:+test+log")
depends_on("bzip2")
depends_on("cpio", type="build")
depends_on("diffutils", type="build")
depends_on("jpeg")
depends_on("libpng")
depends_on("libtiff")
depends_on("libxml2")
depends_on("libxslt@1.1.14:")
depends_on("lzo")
depends_on("pcre")
depends_on("giflib")
depends_on("sqlite@3.6.6:")
depends_on("zlib-api")
depends_on("samtools")
depends_on("bamtools")
depends_on("berkeley-db")
def configure_args(self):
args = ["--without-sybase", "--without-fastcgi"]
if "+debug" not in self.spec:
args += ["--without-debug"]
return args
def patch(self):
with working_dir(join_path("src", "util", "image")):
filter_file(
r"jpeg_start_compress(&cinfo, true)",
"jpeg_start_compress(&cinfo, TRUE)",
"image_io_jpeg.cpp",
string=True,
)
# TODO: Convert these substitutions into BOOST_VERSION preprocessor
# patches to send upstream.
if self.spec.satisfies("@:22_0_0 ^boost@1.69:"):
with working_dir(join_path("include", "corelib")):
filter_file(r"(boost::unit_test::decorator::collector)", r"\1_t", "test_boost.hpp")
if self.spec.satisfies("@:22_0_0 ^boost@1.70:"):
with working_dir(join_path("include", "corelib")):
filter_file(
("unit_test::ut_detail::" "ignore_unused_variable_warning"),
"ignore_unused",
"test_boost.hpp",
string=True,
)
with working_dir(join_path("src", "corelib")):
for file_ in ["test_boost.cpp", "teamcity_boost.cpp"]:
filter_file(
r"(void log_build_info\s*\(.*ostream&[^)]*)\);",
r"\1, bool log_build_info = true);",
file_,
)
filter_file(
r"(::log_build_info\(.*ostream.*&[^)]+)\)",
r"\1, bool log_build_info)",
file_,
)
filter_file(r"(log_build_info\(ostr)\)", r"\1, true)", file_)
with working_dir(join_path("scripts", "common", "impl")):
files = ["if_diff.sh", "update_configurable.sh"]
for file in files:
filter_file("PATH=/bin:/usr/bin", "", file)
def build(self, spec, prefix):
with working_dir(join_path(glob("*MT64")[0], "build")):
make("all_r")
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