From 430b8ca3623cdb15bd30ff196991ab1ec69f5012 Mon Sep 17 00:00:00 2001 From: downloadico Date: Fri, 26 Aug 2022 17:38:27 -0600 Subject: add sra-tools and NCBI-VDT packages (#32403) * ncbi-vdb: add ncbi-vdb package to spack ncbi-vdb provides the interface to the NCBI VDB * sra-tools: add sra-tools to spack --- .../repos/builtin/packages/ncbi-vdb/package.py | 21 ++++++++++++++++ .../repos/builtin/packages/sra-tools/package.py | 29 ++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ncbi-vdb/package.py create mode 100644 var/spack/repos/builtin/packages/sra-tools/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ncbi-vdb/package.py b/var/spack/repos/builtin/packages/ncbi-vdb/package.py new file mode 100644 index 0000000000..cf8136d55c --- /dev/null +++ b/var/spack/repos/builtin/packages/ncbi-vdb/package.py @@ -0,0 +1,21 @@ +# 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") diff --git a/var/spack/repos/builtin/packages/sra-tools/package.py b/var/spack/repos/builtin/packages/sra-tools/package.py new file mode 100644 index 0000000000..2606013c20 --- /dev/null +++ b/var/spack/repos/builtin/packages/sra-tools/package.py @@ -0,0 +1,29 @@ +# 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 -- cgit v1.2.3-60-g2f50