603569e321
* Style: black 23, skip magic trailing commas * isort should use same line length as black * Fix unused import * Update version of black used in CI * Update new packages * Update new packages
183 lines
7.9 KiB
Python
183 lines
7.9 KiB
Python
# Copyright 2013-2023 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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from spack.package import *
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from spack.pkg.builtin.boost import Boost
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class Augustus(MakefilePackage):
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"""AUGUSTUS is a program that predicts genes in eukaryotic
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genomic sequences"""
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homepage = "https://bioinf.uni-greifswald.de/augustus/"
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url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
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# Releases have moved to github
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version("3.4.0", sha256="2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8")
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version("3.3.2", sha256="d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2")
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version(
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"3.3.1-tag1",
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sha256="011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab",
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url="https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz",
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)
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version(
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"3.3",
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sha256="b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee",
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url="https://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz",
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)
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version(
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"3.2.3",
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sha256="a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514",
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url="https://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz",
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)
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depends_on("perl", type=("build", "run"))
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depends_on("python", when="@3.3.1:", type=("build", "run"))
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depends_on("bamtools")
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depends_on("gsl")
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# TODO: replace this with an explicit list of components of Boost,
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# for instance depends_on('boost +filesystem')
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# See https://github.com/spack/spack/pull/22303 for reference
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depends_on(Boost.with_default_variants)
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depends_on("zlib")
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depends_on("htslib")
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depends_on("bcftools")
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depends_on("samtools")
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depends_on("ncurses")
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depends_on("curl", when="@3.3.1:")
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depends_on("sqlite", when="@3.4.0:")
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depends_on("mysql-client", when="@3.4.0:")
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depends_on("mysqlpp", when="@3.4.0:")
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depends_on("lp-solve", when="@3.4.0:")
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depends_on("suite-sparse", when="@3.4.0:")
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# Trying to use filter_file here got too complicated so use a patch with a
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# corresponding environment variable
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patch("bam2wig_Makefile.patch", when="@3.4.0:")
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def edit(self, spec, prefix):
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# Set compile commands for each compiler and
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# Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1)
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if self.version >= Version("3.3.1-tag1"):
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with working_dir(join_path("auxprogs", "utrrnaseq", "Debug")):
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filter_file("g++", spack_cxx, "makefile", string=True)
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filter_file(
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"g++ -I/usr/include/boost",
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"{0} -I{1}".format(spack_cxx, self.spec["boost"].prefix.include),
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"src/subdir.mk",
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string=True,
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)
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# Makefiles to set spack compiler over gcc/g++
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makefiles = [
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"auxprogs/aln2wig/Makefile",
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"auxprogs/bam2hints/Makefile",
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"auxprogs/bam2wig/Makefile",
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"auxprogs/compileSpliceCands/Makefile",
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"auxprogs/homGeneMapping/src/Makefile",
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"auxprogs/joingenes/Makefile",
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"src/Makefile",
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]
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if self.version < Version("3.4.0"):
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makefiles.append("auxprogs/checkTargetSortedness/Makefile")
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if self.version >= Version("3.4.0"):
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makefiles.extend(["auxprogs/filterBam/src/Makefile", "src/unittests/Makefile"])
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for makefile in makefiles:
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filter_file("gcc", spack_cc, makefile, string=True)
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filter_file("g++", spack_cxx, makefile, string=True)
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bamtools = self.spec["bamtools"].prefix
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bcftools = self.spec["bcftools"].prefix
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htslib = self.spec["htslib"].prefix
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samtools = self.spec["samtools"].prefix
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with working_dir(join_path("auxprogs", "filterBam", "src")):
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makefile = FileFilter("Makefile")
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makefile.filter("BAMTOOLS = .*", "BAMTOOLS = {0}".format(bamtools))
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makefile.filter("INCLUDES = *", "INCLUDES = -I$(BAMTOOLS)/include/bamtools ")
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if "bamtools@2.5:" in spec:
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makefile.filter(
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"LIBS = -lbamtools -lz", "LIBS = $(BAMTOOLS)/lib64" "/libbamtools.a -lz"
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)
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if "bamtools@:2.4" in spec:
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makefile.filter(
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"LIBS = -lbamtools -lz", "LIBS = $(BAMTOOLS)/lib/bamtools" "/libbamtools.a -lz"
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)
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with working_dir(join_path("auxprogs", "bam2hints")):
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makefile = FileFilter("Makefile")
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makefile.filter("/usr/include/bamtools", "{0}/include/bamtools".format(bamtools))
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if "bamtools@2.5:" in spec:
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makefile.filter(
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"LIBS = -lbamtools -lz",
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"LIBS = {0}/lib64" "/libbamtools.a -lz".format(bamtools),
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)
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if "bamtools@:2.4" in spec:
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makefile.filter(
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"LIBS = -lbamtools -lz",
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"LIBS = {0}/lib/bamtools" "/libbamtools.a -lz".format(bamtools),
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)
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if self.version < Version("3.4.0"):
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with working_dir(join_path("auxprogs", "bam2wig")):
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makefile = FileFilter("Makefile")
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# point tools to spack installations
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makefile.filter("BCFTOOLS=.*$", "BCFTOOLS={0}/include".format(bcftools))
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makefile.filter("SAMTOOLS=.*$", "SAMTOOLS={0}/include".format(samtools))
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makefile.filter("HTSLIB=.*$", "HTSLIB={0}/include".format(htslib))
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# fix bad linking dirs
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makefile.filter("$(SAMTOOLS)/libbam.a", "$(SAMTOOLS)/../lib/libbam.a", string=True)
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makefile.filter("$(HTSLIB)/libhts.a", "$(HTSLIB)/../lib/libhts.a", string=True)
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with working_dir(join_path("auxprogs", "checkTargetSortedness")):
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makefile = FileFilter("Makefile")
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makefile.filter("SAMTOOLS.*=.*$", "SAMTOOLS={0}/include".format(samtools))
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makefile.filter("LIBS=-lbam", "LIBS=$(SAMTOOLS)/../lib/libbam.a", string=True)
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else:
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mysql = self.spec["mysql-client"].prefix
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mysqlpp = self.spec["mysqlpp"].prefix
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lpsolve = self.spec["lp-solve"].prefix
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with working_dir("src"):
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makefile = FileFilter("Makefile")
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makefile.filter(r"/usr/include/mysql\+\+", "{0}/include/mysql++".format(mysqlpp))
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if "^mariadb-c-client" in spec:
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makefile.filter("/usr/include/mysql", "{0}/include/mariadb".format(mysql))
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else:
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makefile.filter("/usr/include/mysql", "{0}/include/mysql".format(mysql))
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makefile.filter("/usr/include/lpsolve", "{0}/include/lpsolve".format(lpsolve))
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def install(self, spec, prefix):
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install_tree("bin", join_path(self.spec.prefix, "bin"))
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install_tree("config", join_path(self.spec.prefix, "config"))
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install_tree("scripts", join_path(self.spec.prefix, "scripts"))
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@run_after("install")
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def filter_sbang(self):
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with working_dir(self.prefix.scripts):
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pattern = "^#!.*"
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repl = "#!{0}".format(self.spec["perl"].command.path)
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files = glob.glob("*.pl")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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repl = "#!{0}".format(self.spec["python"].command.path)
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files = glob.glob("*.py")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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def setup_build_environment(self, env):
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if self.version >= Version("3.4.0"):
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htslib = self.spec["htslib"].prefix
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env.set("HTSLIBDIR", htslib)
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def setup_run_environment(self, env):
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env.set("AUGUSTUS_CONFIG_PATH", join_path(self.prefix, "config"))
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env.prepend_path("PATH", join_path(self.prefix, "scripts"))
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