Sonlib (#16060)

* sonLib package as required by the HAL toolkit

* cleanup

* Update var/spack/repos/builtin/packages/sonlib/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/sonlib/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

var/spack/repos/builtin/packages/sonlib/package.py

@@ -0,0 +1,47 @@
+# Copyright 2013-2020 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 import *
+import os
+
+
+class Sonlib(MakefilePackage):
+    """sonLib is a compact C/Python library for
+    sequence analysis in bioinformatics."""
+
+    # This is sonlib as needed by the hal package which expects
+    # a side by side compilation
+    #
+    # If you need to use sonlib then you want py-sonlib
+
+    homepage = "https://github.com/ComparativeGenomicsToolkit"
+    url      = "https://github.com/ComparativeGenomicsToolkit/sonLib"
+    git      = "https://github.com/ComparativeGenomicsToolkit/sonLib.git"
+
+    version('master', branch='master')
+    version('2020-04-01', commit='7ebe2ede05a6ee366d93a7a993db69a99943a68f')
+
+    def setup_build_environment(self, env):
+
+        binpath = os.path.join(self.stage.source_path, 'bin')
+        libpath = os.path.join(self.stage.source_path, 'lib')
+
+        env.set('BINDIR', binpath)
+        env.set('LIBDIR', libpath)
+
+    def build(self, spec, prefix):
+
+        binpath = os.path.join(self.stage.source_path, 'bin')
+        libpath = os.path.join(self.stage.source_path, 'lib')
+
+        mkdir(binpath)
+        mkdir(libpath)
+
+        make()
+
+    def install(self, spec, prefix):
+
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)