pbbam: new package (#8365)

* pbbam: new package

* pbbam: updated version

* pbbam: added option tests handling

* pbbam: flake8 edits

1 files changed, 62 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/pbbam/package.py b/var/spack/repos/builtin/packages/pbbam/package.py
new file mode 100644
index 0000000000..f9b1ccc727
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pbbam/package.py
@@ -0,0 +1,62 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Pbbam(CMakePackage):
+    """The pbbam software package provides components to create, query,
+    & edit PacBio BAM files and associated indices.
+    These components include a core C++ library,
+    bindings for additional languages, and command-line utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/pbbam"
+    url      = "https://github.com/PacificBiosciences/pbbam/archive/0.18.0.tar.gz"
+
+    version('0.18.0', 'abbb687b1e7ea08916c26da828e11384')
+
+    depends_on('zlib')
+    depends_on('boost@1.55.0:')
+    depends_on('htslib@1.3.1:')
+    depends_on('doxygen+graphviz')
+
+    conflicts('%gcc@:5.2.0')
+
+    def cmake_args(self):
+        options = []
+        if self.run_tests:
+            options.append('-DPacBioBAM_build_tests:BOOL=ON')
+        else:
+            options.append('-DPacBioBAM_build_tests:BOOL=OFF')
+
+        return options
+
+    def install(self, spec, prefix):
+        install_tree('spack-build/bin', prefix.bin)
+        install_tree('spack-build/lib', prefix.lib)
+        install_tree('include/pbbam', prefix.include.pbbam)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('PacBioBAM_LIBRARIES', self.prefix.lib)
+        spack_env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include)