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# Copyright 2013-2024 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.package import *
class Canu(MakefilePackage):
"""A single molecule sequence assembler for genomes large and
small."""
homepage = "https://canu.readthedocs.io/"
url = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
license("GPL-2.0-only")
version(
"2.2",
sha256="e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404",
url="https://github.com/marbl/canu/releases/download/v2.2/canu-2.2.tar.xz",
)
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("git@2.12:", type="build", when="@2.2:")
depends_on("gnuplot", type="run")
depends_on("java", type="run")
depends_on("perl", type="run")
# version guessed from include date of vendored boost
depends_on("boost@1.60.0:+graph")
conflicts("^boost@1.70.1:", when="@:2.0")
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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