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authorilbiondo <61497728+ilbiondo@users.noreply.github.com>2020-04-15 23:04:06 +0200
committerGitHub <noreply@github.com>2020-04-15 16:04:06 -0500
commite41ac9af8a714c364a24f6d8446fd353c960f41c (patch)
tree06fa6ddb3764bb21255486e4c6362ccec4c68c2c
parentfef4e80a6ddcd4ea0841a21be2b9ed857519e40f (diff)
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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>
-rw-r--r--var/spack/repos/builtin/packages/sonlib/package.py47
1 files changed, 47 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sonlib/package.py b/var/spack/repos/builtin/packages/sonlib/package.py
new file mode 100644
index 0000000000..c071e8a7b0
--- /dev/null
+++ b/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)