45 lines
1.6 KiB
Python
45 lines
1.6 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Tophat(AutotoolsPackage):
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"""Spliced read mapper for RNA-Seq."""
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homepage = "https://ccb.jhu.edu/software/tophat/index.shtml"
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url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
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license("BSL-1.0")
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version("2.1.2", sha256="15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1")
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version("2.1.1", sha256="991b1b7c840a5f5c4e9a15b2815983257d2b0748246af0b9094c7d07552b023e")
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depends_on("c", type="build") # generated
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depends_on("cxx", type="build") # generated
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depends_on("autoconf", type="build")
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# 2.1.1 only builds with automake@1.15.1. There's a patch here:
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# https://github.com/spack/spack/pull/8244, which was incorporated
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# upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
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depends_on("automake", type="build")
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depends_on("automake@1.15.1", when="@:2.1.1", type="build")
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depends_on("libtool", type="build")
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depends_on("m4", type="build")
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depends_on("boost@1.47:+exception+chrono+system+random+atomic+thread")
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depends_on("bowtie2", type="run")
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parallel = False
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def patch(self):
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# Newer versions of autoconf hate calling AM_INIT_AUTOMAKE twice
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filter_file(r"^AM_INIT_AUTOMAKE$", "", "configure.ac")
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def setup_build_environment(self, env):
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env.append_flags("CFLAGS", self.compiler.cxx98_flag)
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def configure_args(self):
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return ["--with-boost={0}".format(self.spec["boost"].prefix)]
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