1 files changed, 54 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
new file mode 100644
index 0000000000..ceb7d642ff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 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 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)