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# 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 Canu(MakefilePackage):
"""A single molecule sequence assembler for genomes large and
small."""
homepage = "http://canu.readthedocs.io/"
url = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
version('2.0', sha256='e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef')
version('1.8', sha256='30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4')
version('1.7.1', sha256='c314659c929ee05fd413274f391463a93f19b8337eabb7ee5de1ecfc061caafa')
version('1.7', sha256='c5be54b0ad20729093413e7e722a19637d32e966dc8ecd2b579ba3e4958d378a')
version('1.5', sha256='06e2c6d7b9f6d325b3b468e9c1a5de65e4689aed41154f2cee5ccd2cef0d5cf6')
depends_on('gnuplot', type='run')
depends_on('java', type='run')
depends_on('perl', type='run')
# build fail when using boost@1.71.0:1.73.0 by canu@1.8:2.0
depends_on('boost@:1.70.0')
build_directory = 'src'
build_targets = ['clean']
def patch(self):
# Use our perl, not whatever is in the environment
filter_file(r'^#!/usr/bin/env perl',
'#!{0}'.format(self.spec['perl'].command.path),
'src/pipelines/canu.pl')
def install(self, spec, prefix):
with working_dir(self.build_directory):
make('all', 'TARGET_DIR={0}'.format(prefix))
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