eda5b854a5
* This commit removes the Boost.with_default_variants to variants that packages are precisely dependant upon. This is the first batch of 20 packages with modified boost dependencies. * Style fixes * Tested bridger: works for gcc-4.9.3 and gcc-8.3.1
40 lines
1.4 KiB
Python
40 lines
1.4 KiB
Python
# 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'))
|