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# Copyright 2013-2022 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 os import symlink
from spack import *
class Bridger(MakefilePackage, SourceforgePackage):
"""Bridger : An Efficient De novo Transcriptome Assembler For
RNA-Seq Data"""
homepage = "https://sourceforge.net/projects/rnaseqassembly/"
sourceforge_mirror_path = "rnaseqassembly/Bridger_r2014-12-01.tar.gz"
version('2014-12-01', sha256='8fbec8603ea8ad2162cbd0c658e4e0a4af6453bdb53310b4b7e0d112e40b5737')
depends_on('boost + exception + filesystem + system + serialization + graph')
depends_on('perl', type='run')
def flag_handler(self, name, flags):
if name == 'cflags':
# some of the plugins require gnu extensions
flags.append('-std=gnu99')
if name == 'cxxflags':
flags.append('-std=c++03')
return (flags, None, None)
def install(self, spec, prefix):
# bridger depends very much on perl scripts/etc in the source tree
install_path = join_path(prefix, 'usr/local/bridger')
mkdirp(install_path)
install_tree('.', install_path)
# symlink the init script to /bin
mkdirp(prefix.bin)
symlink(join_path(install_path, 'Bridger.pl'),
join_path(prefix.bin, 'Bridger.pl'))
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