blasr: new package (#8367)

* blasr: new package

* blasr: changed version release, created list with 9 things, seperated make into build phase.

* blasr: fixed build phase by adding :

* blasr: fixed syntax for configure_args

* blasr: flake8 edits

* blasr-libcpp: fixed configure_args syntax

* blasr: fixed install issues resulting from PacBio changes

* blasr: removed accidental blasr-libcpp upload

* blasr: removed accidental blasr-libcpp upload

* blasr: removed blasr-libcpp

* blasr: edited out comment

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

+##############################################################################
+# 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 Blasr(Package):
+    """The PacBio long read aligner."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr/wiki"
+    url      = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
+
+    version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') 
+
+    depends_on('ncurses')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    depends_on('htslib')
+    depends_on('zlib')
+    depends_on('boost')
+    depends_on('pbbam')
+    depends_on('blasr-libcpp')
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix.utils)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.pbdata)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.alignment)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
+
+        # hdf has +mpi by default, so handle that possibility
+        if ('+mpi' in self.spec['hdf5']):
+            spack_env.set('CC', self.spec['mpi'].mpicc)
+            spack_env.set('CXX', self.spec['mpi'].mpicxx)
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'LIBPBDATA_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBDATA_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.pbdata),
+            'LIBBLASR_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.alignment),
+            'LIBBLASR_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
+            '--shared'
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = join_path(
+            self.stage.source_path, 'include')
+        make()
+
+    def install(self, spec, prefix):
+        mkdir(prefix.utils)
+        mkdir(prefix.bin)
+        install('blasr', prefix.bin.blasr)
+        install('utils/loadPulses', prefix.utils)
+        install('utils/pls2fasta', prefix.utils)
+        install('utils/samFilter', prefix.utils)
+        install('utils/samtoh5', prefix.utils)
+        install('utils/samtom4', prefix.utils)
+        install('utils/sawriter', prefix.utils)
+        install('utils/sdpMatcher', prefix.utils)
+        install('utils/toAfg', prefix.utils)