72 lines
2.7 KiB
Python
72 lines
2.7 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 Biopieces(Package):
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"""The Biopieces are a collection of bioinformatics tools that can be
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pieced together in a very easy and flexible manner to perform both
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simple and complex tasks."""
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homepage = "https://maasha.github.io/biopieces/"
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git = "https://github.com/maasha/biopieces.git"
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license("GPL-2.0-only")
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version("2016-04-12", commit="982f80f7c55e2cae67737d80fe35a4e784762856", submodules=True)
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depends_on("perl", type=("build", "run"))
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depends_on("perl-module-build", type=("build", "run"))
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depends_on("perl-bit-vector", type=("build", "run"))
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depends_on("perl-svg", type=("build", "run"))
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depends_on("perl-termreadkey", type=("build", "run"))
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depends_on("perl-time-hires", type=("build", "run"))
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depends_on("perl-dbi", type=("build", "run"))
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depends_on("perl-xml-parser", type=("build", "run"))
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depends_on("perl-carp-clan", type=("build", "run"))
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depends_on("perl-class-inspector", type=("build", "run"))
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depends_on("perl-html-parser", type=("build", "run"))
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depends_on("perl-libwww-perl", type=("build", "run"))
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depends_on("perl-soap-lite", type=("build", "run"))
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depends_on("perl-uri", type=("build", "run"))
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depends_on("perl-inline", type=("build", "run"))
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depends_on("perl-inline-c", type=("build", "run"))
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depends_on("perl-parse-recdescent", type=("build", "run"))
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depends_on("perl-perl-version", type=("build", "run"))
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depends_on("perl-db-file", type=("build", "run"))
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depends_on("perl-dbd-mysql", type=("build", "run"))
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depends_on("ruby@1.9:")
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depends_on("ruby-gnuplot")
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depends_on("ruby-narray")
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depends_on("ruby-rubyinline")
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depends_on("ruby-terminal-table")
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depends_on("python@2.6:", type=("build", "run"))
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depends_on("blast-plus")
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depends_on("muscle")
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depends_on("mummer")
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depends_on("blat")
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depends_on("vmatch")
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depends_on("bowtie")
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depends_on("bwa")
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depends_on("usearch")
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depends_on("velvet")
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depends_on("idba")
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depends_on("ray")
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depends_on("scan-for-matches")
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def install(self, spec, prefix):
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install_tree(".", prefix)
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def setup_run_environment(self, env):
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# Note: user will need to set environment variables on their own,
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# dependent on where they will want data to be located:
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# BP_DATA - Contains genomic data etc.
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# BP_TMP - Required temporary directory
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# BP_LOG - Required log directory
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env.prepend_path("BP_DIR", self.prefix)
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