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add sra-tools and NCBI-VDT packages (#32403)

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* ncbi-vdb: add ncbi-vdb package to spack
ncbi-vdb provides the interface to the NCBI VDB

* sra-tools: add sra-tools to spack
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downloadico 2022-08-26 17:38:27 -06:00 committed by GitHub
parent e6f6de406d
commit 430b8ca362
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var/spack/repos/builtin/packages/ncbi-vdb/package.py Normal file
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# Copyright 2013-2022 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 NcbiVdb(CMakePackage):
"""The SRA Toolkit and SDK from NCBI is a collection of tools and
libraries for using data in the INSDC Sequence Read Archives.
This package contains the interface to the VDB."""
homepage = "https://github.com/ncbi/ncbi-vdb"
git = "https://github.com/ncbi/ncbi-vdb.git"
version("3.0.0", tags="3.0.0")
depends_on("openjdk")
depends_on("flex@2.6:")
depends_on("libxml2")

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var/spack/repos/builtin/packages/sra-tools/package.py Normal file
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# Copyright 2013-2022 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("3.0.0", tags="3.0.0")
depends_on("openjdk")
depends_on("flex@2.6:")
depends_on("libxml2")
depends_on("ncbi-vdb")
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