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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 *
def is_positive_int(x):
if x.isdigit() and int(x) > 0:
return True
else:
return False
class Velvet(MakefilePackage):
"""Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies."""
homepage = "https://www.ebi.ac.uk/~zerbino/velvet/"
url = "https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz"
maintainers("snehring")
license("GPL-2.0-only")
version("1.2.10", sha256="884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640")
variant(
"categories",
default="2",
description="Number of channels which can be handled independently",
values=is_positive_int,
)
variant(
"maxkmerlength",
default="31",
description="Longest kmer size you can use in an analysis",
values=is_positive_int,
)
variant("bigassembly", default=False, description="Allow assemblies with more than 2^31 reads")
variant(
"vbigassembly",
default=False,
description="Allow unsigned 64-bit array index values (also enables bigassembly)",
)
variant(
"longsequences", default=False, description="Allow assembling contigs longer than 32kb"
)
variant("openmp", default=False, description="Enable multithreading")
variant("single_cov_cat", default=False, description="Per-library coverage")
depends_on("zlib-api")
def edit(self, spec, prefix):
makefile = FileFilter("Makefile")
if spec.target.family == "aarch64":
makefile.filter("-m64", "")
maxkmerlength = self.spec.variants["maxkmerlength"].value
categories = self.spec.variants["categories"].value
makefile.filter(r"^MAXKMERLENGTH\s*=\s*.*", f"MAXKMERLENGTH = {maxkmerlength}")
makefile.filter(r"^CATEGORIES\s*=\s*.*", f"CATEGORIES = {categories}")
if "+bigassembly" in self.spec:
makefile.filter("^ifdef BIGASSEMBLY", "BIGASSEMBLY=1\nifdef BIGASSEMBLY")
if "+vbigassembly" in self.spec:
makefile.filter("^ifdef VBIGASSEMBLY", "VBIGASSEMBLY=1\nifdef VBIGASSEMBLY")
if "+longsequences" in self.spec:
makefile.filter("^ifdef LONGSEQUENCES", "LONGSEQUENCES=1\nifdef LONGSEQUENCES")
if "+openmp" in self.spec:
makefile.filter("^ifdef OPENMP", "OPENMP=1\nifdef OPENMP")
if "+single_cov_cat" in self.spec:
makefile.filter("^ifdef SINGLE_COV_CAT", "SINGLE_COV_CAT=1\nifdef SINGLE_COV_CAT")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("velvetg", prefix.bin)
install("velveth", prefix.bin)
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