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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 SoapdenovoTrans(MakefilePackage):
"""SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
SOAPdenovo framework, adapt to alternative splicing and different
expression level among transcripts."""
homepage = "https://github.com/aquaskyline/SOAPdenovo-Trans"
url = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
maintainers("snehring")
license("GPL-3.0-only")
version("1.0.5", sha256="c1903c0d81142270db95916e2833400f72c4841b5c9194f182c19ebda418936f")
version("1.0.4", sha256="378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795")
depends_on("zlib-api", type="link")
depends_on("samtools@0.1.8", type="link", when="target=aarch64:")
build_directory = "src"
def edit(self, spec, prefix):
with working_dir(self.build_directory):
makefile = FileFilter("Makefile")
makefile.filter(
"CFLAGS= -O3 -fomit-frame-pointer -static",
"CFLAGS= -O3 -fomit-frame-pointer",
)
if spec.target.family == "aarch64":
makefile.filter("ppc64 ia64", "ppc64 ia64 aarch64")
def build(self, spec, prefix):
with working_dir(self.build_directory):
make()
make("127mer=1", parallel=False)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("SOAPdenovo-Trans-*mer", prefix.bin)
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