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# Copyright 2013-2023 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 spack.package import *
class NcbiRmblastn(AutotoolsPackage):
"""RMBlast search engine for NCBI"""
homepage = "https://www.repeatmasker.org/rmblast/"
url = (
"https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz"
)
version("2.14.0", sha256="bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500")
version("2.11.0", sha256="d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954")
version("2.9.0", sha256="a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257")
maintainers("snehring")
# There is a corresponding gzipped patch file associated with each version.
# According to the documentation, https://www.repeatmasker.org/RMBlast.html,
# Download NCBI Blast+ and rmblast patch file:
# ncbi-blast-2.11.0+-src.tar.gz
# isb-2.11.0+-rmblast.patch.gz
# The patch is downloaded and unzipped in the ncbi-rmblastn Spack package
# directory to make it available for the patch directive.
patch(
"https://www.repeatmasker.org/rmblast/isb-2.14.0+-rmblast.patch.gz",
sha256="cd083f256551c6d6021897a1b08e023976e82c59576787d4885f57d36f9e6fdf",
archive_sha256="9de0e67467a4cffdde0c5f67e3658fb52ed313e4550f9a36a251bddb2ba33f49",
when="@2.14.0",
)
patch(
"https://www.repeatmasker.org/isb-2.11.0+-rmblast.patch.gz",
sha256="ce985abd3512834adb9ad3e4078fbf9608a33a2ee6538a1e94b641490c92f899",
archive_sha256="0fc27781c2ea2f17645247e2f3775b5d18c56f0b62761a865347be745ea4f6be",
when="@2.11.0",
)
patch(
"https://www.repeatmasker.org/isb-2.9.0+-rmblast.patch.gz",
sha256="ffa0845801aed11f4215b452532f3ff5b3dcb49ac8c14169568aaa585b9450ed",
archive_sha256="e746ee480ade608052306fd21f015c8a323f27029f65399275216f9a4c882d59",
when="@2.9.0",
)
patch("gcc13.patch", level=0, when="@2.14.0:%gcc@13:")
depends_on("cpio", type="build")
depends_on("boost")
depends_on("lzo")
depends_on("bzip2")
depends_on("zstd")
depends_on("xz")
configure_directory = "c++"
def url_for_version(self, version):
url = (
"https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{0}/ncbi-blast-{1}+-src.tar.gz"
)
return url.format(version, version)
def configure_args(self):
args = [
"--with-mt",
"--without-debug",
"--without-krb5",
"--without-openssl",
"--without-libuv",
"--with-projects=scripts/projects/rmblastn/project.lst",
]
return args
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