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

2 files changed, 50 insertions, 0 deletions

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