102 lines
3.6 KiB
Python
102 lines
3.6 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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class Repeatmasker(Package):
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"""RepeatMasker is a program that screens DNA sequences for interspersed
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repeats and low complexity DNA sequences."""
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homepage = "https://www.repeatmasker.org"
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version("4.1.2-p1", sha256="4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96")
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version("4.0.9", sha256="8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5")
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version("4.0.7", sha256="16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166")
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variant("crossmatch", description="Enable CrossMatch search engine", default=False)
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depends_on("perl", type=("build", "run"))
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depends_on("perl-text-soundex", type=("build", "run"))
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depends_on("hmmer")
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depends_on("ncbi-rmblastn")
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depends_on("trf")
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depends_on("python", when="@4.1:", type=("build", "run"))
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depends_on("py-h5py", when="@4.1:", type=("build", "run"))
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depends_on("phrap-crossmatch-swat", type=("build", "run"), when="+crossmatch")
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patch("utf8.patch", when="@:4.0")
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def url_for_version(self, version):
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if version >= Version("4.1.0"):
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url = "http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz"
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return url.format(version)
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else:
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url = "http://www.repeatmasker.org/RepeatMasker/RepeatMasker-open-{0}.tar.gz"
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return url.format(version.dashed)
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def install(self, spec, prefix):
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# Config questions consist of:
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#
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# <PRESS ENTER TO CONTINUE>
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# Enter perl path
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# Enter where repeatmasker is being configured from
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# Enter trf path
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# Add a Search Engine:
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# 1. CrossMatch
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# 2. RMBlast - NCBI Blast with RepeatMasker extensions
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# 3. WUBlast/ABBlast (required by DupMasker)
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# 4. HMMER3.1 & DFAM
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# 5. Done
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# Enter RMBlast path
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# Do you want RMBlast to be your default search engine for
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# Repeatmasker? (Y/N)
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# Add a Search Engine: Done
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config_answers = []
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if spec.satisfies("@:4.0.7"):
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# 4.0.9 removes a bunch of the interactive options
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config_answers.extend(["", self.spec["perl"].command.path, self.stage.source_path])
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# set path to trf
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config_answers.append(self.spec["trf"].prefix.bin.trf)
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# add crossmatch search
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if "+crossmatch" in spec:
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crossmatch = self.spec["phrap-crossmatch-swat"].prefix.bin
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config_answers.extend(["1", crossmatch, "N"])
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# set default BLAST search
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config_answers.extend(["2", self.spec["ncbi-rmblastn"].prefix.bin, "Y"])
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# set non-default HMMER search
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if spec.satisfies("@4.0.9:"):
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config_answers.extend(["3", self.spec["hmmer"].prefix.bin, "N"])
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else:
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config_answers.extend(["4", self.spec["hmmer"].prefix.bin, "N"])
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# end configuration
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config_answers.append("5")
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config_answers_filename = "spack-config.in"
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with open(config_answers_filename, "w") as f:
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f.write("\n".join(config_answers))
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with open(config_answers_filename, "r") as f:
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perl = which("perl")
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perl("configure", input=f)
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# fix perl paths
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# every sbang points to perl, so a regex will suffice
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for f in glob.glob("*.pm"):
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filter_file("#!.*", "#!%s" % spec["perl"].command, f)
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install_tree(".", prefix.bin)
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