From 53c0c5701c364ebdd10f56d7063a693d2059ff15 Mon Sep 17 00:00:00 2001
From: Miles Perry <37849532+Miles-Perry@users.noreply.github.com>
Date: Sat, 7 Jul 2018 10:05:57 -0500
Subject: [PATCH] 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
---
.../repos/builtin/packages/blasr/package.py | 96 +++++++++++++++++++
1 file changed, 96 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/blasr/package.py
diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py
new file mode 100644
index 0000000000..b7f100b642
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr/package.py
@@ -0,0 +1,96 @@
+##############################################################################
+# 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)
--
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