# 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 Shortstack(Package):
    """ShortStack is a tool developed to process and analyze smallRNA-seq data
    with respect to a reference genome, and output a comprehensive and
    informative annotation of all discovered small RNA genes."""

    homepage = "https://sites.psu.edu/axtell/software/shortstack/"
    url = "https://github.com/MikeAxtell/ShortStack/archive/v3.8.3.tar.gz"

    license("MIT")

    version("4.0.1", sha256="d8ca2d5b245d13c9f2b2e6fa06bc34bc8f6bacbe07efebe3750b0178141cbeb6")
    version("3.8.3", sha256="7c76f51ed949ca95ec5df7cb54803ae2350658fd64c75909351d5a856abb0dbe")

    depends_on("perl", type=("build", "run"))
    depends_on("samtools")
    depends_on("viennarna")
    depends_on("bowtie")

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install("ShortStack", prefix.bin)