24c01d57cf
* fix remaining flake8 errors * imports: sort imports everywhere in Spack We enabled import order checking in #23947, but fixing things manually drives people crazy. This used `spack style --fix --all` from #24071 to automatically sort everything in Spack so PR submitters won't have to deal with it. This should go in after #24071, as it assumes we're using `isort`, not `flake8-import-order` to order things. `isort` seems to be more flexible and allows `llnl` mports to be in their own group before `spack` ones, so this seems like a good switch.
48 lines
1.8 KiB
Python
48 lines
1.8 KiB
Python
# Copyright 2013-2021 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)
|
|
|
|
import glob
|
|
import os.path
|
|
|
|
from spack import *
|
|
|
|
|
|
class Express(CMakePackage):
|
|
"""eXpress is a streaming tool for quantifying the abundances of a set of
|
|
target sequences from sampled subsequences."""
|
|
|
|
homepage = "http://bio.math.berkeley.edu/eXpress/"
|
|
url = "https://github.com/adarob/eXpress/archive/1.5.2.zip"
|
|
|
|
# 1.5.1 used to be known as 2015-11-29 (same commit), but they've
|
|
# added tags, so lets use 'em
|
|
version('1.5.2', sha256='25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e')
|
|
version('1.5.1', sha256='fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293')
|
|
|
|
depends_on('boost')
|
|
depends_on('bamtools')
|
|
depends_on('zlib')
|
|
|
|
# patch from the debian package repo:
|
|
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859
|
|
patch('gcc-6.patch', when='%gcc@6.0.0:')
|
|
patch('gcc-6.patch', when='%fj')
|
|
|
|
def patch(self):
|
|
with working_dir('src'):
|
|
files = glob.iglob('*.*')
|
|
for file in files:
|
|
if os.path.isfile(file):
|
|
edit = FileFilter(file)
|
|
edit.filter('#include <api', '#include <%s' % self.spec[
|
|
'bamtools'].prefix.include.bamtools.api)
|
|
edit = FileFilter('CMakeLists.txt')
|
|
edit.filter(r'\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
|
|
'libbamtools.a', '%s' % self.spec['bamtools'].libs)
|
|
|
|
def setup_build_environment(self, env):
|
|
env.prepend_path('CPATH',
|
|
self.spec['bamtools'].prefix.include.bamtools)
|