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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 os import symlink
from spack.package 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"
license("GPL-2.0-only")
version(
"2014-12-01", sha256="8fbec8603ea8ad2162cbd0c658e4e0a4af6453bdb53310b4b7e0d112e40b5737"
)
depends_on("boost + exception + filesystem + system + serialization + graph")
depends_on("ncurses~termlib")
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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