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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Biopieces(Package):
"""The Biopieces are a collection of bioinformatics tools that can be
pieced together in a very easy and flexible manner to perform both
simple and complex tasks."""
homepage = "https://maasha.github.io/biopieces/"
git = "https://github.com/maasha/biopieces.git"
license("GPL-2.0-only")
version("2016-04-12", commit="982f80f7c55e2cae67737d80fe35a4e784762856", submodules=True)
depends_on("perl", type=("build", "run"))
depends_on("perl-module-build", type=("build", "run"))
depends_on("perl-bit-vector", type=("build", "run"))
depends_on("perl-svg", type=("build", "run"))
depends_on("perl-termreadkey", type=("build", "run"))
depends_on("perl-time-hires", type=("build", "run"))
depends_on("perl-dbi", type=("build", "run"))
depends_on("perl-xml-parser", type=("build", "run"))
depends_on("perl-carp-clan", type=("build", "run"))
depends_on("perl-class-inspector", type=("build", "run"))
depends_on("perl-html-parser", type=("build", "run"))
depends_on("perl-libwww-perl", type=("build", "run"))
depends_on("perl-soap-lite", type=("build", "run"))
depends_on("perl-uri", type=("build", "run"))
depends_on("perl-inline", type=("build", "run"))
depends_on("perl-inline-c", type=("build", "run"))
depends_on("perl-parse-recdescent", type=("build", "run"))
depends_on("perl-perl-version", type=("build", "run"))
depends_on("perl-db-file", type=("build", "run"))
depends_on("perl-dbd-mysql", type=("build", "run"))
depends_on("ruby@1.9:")
depends_on("ruby-gnuplot")
depends_on("ruby-narray")
depends_on("ruby-rubyinline")
depends_on("ruby-terminal-table")
depends_on("python@2.6:", type=("build", "run"))
depends_on("blast-plus")
depends_on("muscle")
depends_on("mummer")
depends_on("blat")
depends_on("vmatch")
depends_on("bowtie")
depends_on("bwa")
depends_on("usearch")
depends_on("velvet")
depends_on("idba")
depends_on("ray")
depends_on("scan-for-matches")
def install(self, spec, prefix):
install_tree(".", prefix)
def setup_run_environment(self, env):
# Note: user will need to set environment variables on their own,
# dependent on where they will want data to be located:
# BP_DATA - Contains genomic data etc.
# BP_TMP - Required temporary directory
# BP_LOG - Required log directory
env.prepend_path("BP_DIR", self.prefix)
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