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# Copyright 2013-2018 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 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 = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
url = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')
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')
def build(self, spec, prefix):
with working_dir(self.build_directory):
make()
make('127mer=1', parallel=False)
def install(self, spec, prefix):
install_tree('.', prefix.bin)
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