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# Copyright 2013-2023 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.package 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"
license("Artistic-2.0")
# 1.5.1 used to be known as 2015-11-29 (same commit), but they've
# added tags, so lets use 'em
version("1.5.3", sha256="dfea819bbe7187a06462d6549a13f9cad7f3f128cb5c62bd90946f972c45a1f2")
version("1.5.2", sha256="25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e")
version("1.5.1", sha256="fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293")
depends_on(
"boost"
"+date_time+exception+filesystem+system+chrono"
"+atomic+container+math+thread+program_options"
)
depends_on("bamtools")
depends_on("zlib-api")
# patch from the debian package repo:
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859
patch("gcc-6.patch", when="@:1.5.2%gcc@6.0.0:")
patch("gcc-6.patch", when="@:1.5.2%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)
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