1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
# Copyright 2013-2020 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 *
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', sha256='45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a')
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):
with working_dir(self.build_directory):
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)
install_tree('pbbam', prefix.include.pbbam)
def setup_dependent_build_environment(self, env, dependent_spec):
env.set('PacBioBAM_LIBRARIES', self.prefix.lib)
env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include)
|
