blasr-libcpp: new package (#8366)

* blasr-libcpp: new package

* blasr-libcpp: added version #, and moved make into build phase.

* blasr-libcpp: added prefix.include to PBBAM_INC, added version URL

* blasr-libcpp: indented comments, made list of configure_args, and added prefix.include

* blasr-libcpp: added setup_dependent_environment from blasr

* blasr-libcpp: fixed syntax for configure_args

* blasr-libcpp: fixed configure_args syntax

* blasr-libcpp: fixed syntax

* blasr-libcpp: syntaxtest

* blasr-libcpp: fixed def build error

* blasr-libcpp: edited dependent environment to move after install phase

* blasr-libcpp: rearranged build and install

* blasr-libcpp: added configure_args

* blasr-libcpp: fixed syntax error

* blasr-libcpp: removed .spec from INC and LIB alignment, pbdata, hdf

* blasr-libcpp: seperated configure args

* blasr-libcpp: edited configure and setup_dependent steps

* blasr-libcpp: added CPATH arg

* blasr-libcpp: C_INCLUDE_PATH

* blasr-libcpp: fixed install issues resulting from PacBio change

var/spack/repos/builtin/packages/blasr-libcpp/package.py

@@ -0,0 +1,73 @@
+##############################################################################
+# 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 *
+import os
+
+
+class BlasrLibcpp(Package):
+    """Blasr_libcpp is a library used by blasr
+    and other executables such as samtoh5,
+    loadPulses for analyzing PacBio sequences."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
+    url      = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
+
+    version('5.3.1', 'ca770042cbca508d5ff12dff0d645045')
+
+    depends_on('pbbam')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    # maximum version is 1.8.20 currently. There doesn't appear to be a
+    # major version 1.9 and the 1.10.1 version doesn't build correctly.
+    # https://github.com/PacificBiosciences/blasr/issues/355
+
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'PBBAM_INC={0}'.format(self.spec['pbbam'].prefix.include),
+            'PBBAM_LIB={0}'.format(self.spec['pbbam'].prefix.lib),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib)
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = self.stage.source_path
+        make()
+
+    def install(self, spec, prefix):
+        install_tree('alignment', prefix.alignment)
+        install_tree('hdf', prefix.hdf)
+        install_tree('pbdata', prefix.pbdata)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.hdf)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.alignment)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.pbdata)