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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 spack.package import *
class SraTools(CMakePackage):
"""The SRA Toolkit and SDK from NCBI is a collection of tools and
libraries for using data in the INSDC Sequence Read Archives."""
homepage = "https://github.com/ncbi/sra-tools"
git = "https://github.com/ncbi/sra-tools.git"
version("3.0.3", tag="3.0.3", commit="01f0aa21bb20b84c68ea34404d43da680811e27a")
version("3.0.0", tag="3.0.0", commit="bd2053a1049e64207e75f4395fd1be7f1572a5aa")
depends_on("openjdk")
depends_on("flex@2.6:")
depends_on("libxml2")
depends_on("ncbi-vdb")
depends_on("ncbi-vdb@3.0.2:", when="@3.0.3:")
# The CMakeLists.txt file set the path to ${TARGDIR}/obj but the code
# actually uses ${TARGDIR}.
patch("ngs-java.patch")
def cmake_args(self):
args = [
self.define("VDB_INCDIR", format(self.spec["ncbi-vdb"].prefix) + "/include"),
self.define("VDB_LIBDIR", format(self.spec["ncbi-vdb"].prefix) + "/lib64"),
self.define("VDB_BINDIR", format(self.spec["ncbi-vdb"].prefix)),
]
return args
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