41 lines
1.4 KiB
Python
41 lines
1.4 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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from os import symlink
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from spack.package import *
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class LtrRetriever(Package):
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"""LTR_retriever is a highly accurate and sensitive program for
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identification of LTR retrotransposons."""
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homepage = "https://github.com/oushujun/LTR_retriever"
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url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"
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version("2.8.7", sha256="29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369")
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depends_on("perl", type="run")
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depends_on("blast-plus", type="run")
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depends_on("hmmer@3.1b2:", type="run")
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depends_on("cdhit", type="run")
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depends_on("repeatmasker", type="run")
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def install(self, spec, prefix):
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filter_file(r"BLAST\+=.*", "BLAST+=%s" % spec["blast-plus"].prefix.bin, "paths")
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filter_file(
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"RepeatMasker=.*", "RepeatMasker=%s" % spec["repeatmasker"].prefix.bin, "paths"
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)
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filter_file("HMMER=.*", "HMMER=%s" % spec["hmmer"].prefix.bin, "paths")
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filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix, "paths")
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filter_file("BLAST=.*", "", "paths")
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mkdirp(prefix.opt)
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mkdirp(prefix.bin)
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install_tree(".", prefix.opt.ltr_retriever)
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symlink(prefix.opt.ltr_retriever.LTR_retriever, prefix.bin.LTR_retriever)
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