76 lines
2.8 KiB
Python
76 lines
2.8 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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from spack.package import *
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class Isescan(Package):
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"""A python pipeline to identify IS (Insertion Sequence) elements in
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genome and metagenome"""
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homepage = "https://github.com/xiezhq/ISEScan"
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url = "https://github.com/xiezhq/ISEScan/archive/refs/tags/v1.7.2.1.tar.gz"
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license("Apache-2.0")
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version("1.7.2.3", sha256="90ef6bc660e471347f65864bd3563f769ed4b79b1a932195f353c5e86351ab05")
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version("1.7.2.1", sha256="b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d")
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depends_on("python@3.3.3:", type="run")
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depends_on("py-numpy@1.8.0:", type="run")
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depends_on("py-scipy@0.13.1:", type="run")
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depends_on("py-biopython@1.62:", type="run")
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depends_on("py-fastcluster", type="run")
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depends_on("blast-plus@2.2.31:", type="run")
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depends_on("fraggenescan@:1.30", type="run")
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depends_on("hmmer@3.1b2:", type="run")
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def setup_run_environment(self, env):
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env.prepend_path("PATH", self.prefix)
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env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "ssw201507"))
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def install(self, spec, prefix):
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# build bundled SSW library
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with working_dir("ssw201507"):
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Executable(spack_cc)(
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"-O3",
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"-pipe",
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self.compiler.cc_pic_flag,
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"-shared",
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"-rdynamic",
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"-o",
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"libssw." + dso_suffix,
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"ssw.c",
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"ssw.h",
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)
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# set paths to required programs
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blast_pfx = self.spec["blast-plus"].prefix.bin
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blastn_path = blast_pfx.blastn
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blastp_path = blast_pfx.blastp
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makeblastdb_path = blast_pfx.makeblastdb
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hmmer_pfx = self.spec["hmmer"].prefix.bin
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phmmer_path = hmmer_pfx.phmmer
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hmmsearch_path = hmmer_pfx.hmmsearch
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fgs_pfx = self.spec["fraggenescan"].prefix.bin
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fgs_path = join_path(fgs_pfx, "run_FragGeneScan.pl")
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constants = FileFilter("constants.py")
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constants.filter("/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl", fgs_path, string=True)
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constants.filter("/apps/inst/hmmer-3.3/bin/phmmer", phmmer_path, string=True)
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constants.filter("/apps/inst/hmmer-3.3/bin/hmmsearch", hmmsearch_path, string=True)
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constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastn", blastn_path, string=True)
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constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastp", blastp_path, string=True)
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constants.filter(
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"/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb", makeblastdb_path, string=True
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)
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# install the whole tree
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install_tree(".", prefix)
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set_executable(join_path(prefix, "isescan.py"))
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