58 lines
2.1 KiB
Python
58 lines
2.1 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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import os.path
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from spack.package import *
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class Express(CMakePackage):
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"""eXpress is a streaming tool for quantifying the abundances of a set of
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target sequences from sampled subsequences."""
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homepage = "http://bio.math.berkeley.edu/eXpress/"
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url = "https://github.com/adarob/eXpress/archive/1.5.2.zip"
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license("Artistic-2.0")
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# 1.5.1 used to be known as 2015-11-29 (same commit), but they've
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# added tags, so lets use 'em
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version("1.5.3", sha256="dfea819bbe7187a06462d6549a13f9cad7f3f128cb5c62bd90946f972c45a1f2")
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version("1.5.2", sha256="25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e")
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version("1.5.1", sha256="fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293")
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depends_on(
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"boost"
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"+date_time+exception+filesystem+system+chrono"
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"+atomic+container+math+thread+program_options"
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)
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depends_on("bamtools")
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depends_on("zlib-api")
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# patch from the debian package repo:
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# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859
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patch("gcc-6.patch", when="@:1.5.2%gcc@6.0.0:")
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patch("gcc-6.patch", when="@:1.5.2%fj")
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def patch(self):
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with working_dir("src"):
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files = glob.iglob("*.*")
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for file in files:
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if os.path.isfile(file):
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edit = FileFilter(file)
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edit.filter(
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"#include <api",
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"#include <%s" % self.spec["bamtools"].prefix.include.bamtools.api,
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)
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edit = FileFilter("CMakeLists.txt")
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edit.filter(
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r"\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/" "libbamtools.a",
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"%s" % self.spec["bamtools"].libs,
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)
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def setup_build_environment(self, env):
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env.prepend_path("CPATH", self.spec["bamtools"].prefix.include.bamtools)
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