# 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 Rsem(MakefilePackage):
    """RSEM is a software package for estimating gene and isoform expression
    levels from RNA-Seq data."""

    homepage = "https://deweylab.github.io/RSEM/"
    url = "https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz"

    license("GPL-3.0-or-later")

    version("1.3.3", sha256="90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc")
    version("1.3.1", sha256="93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11")
    version("1.3.0", sha256="ecfbb79c23973e1c4134f05201f4bd89b0caf0ce4ae1ffd7c4ddc329ed4e05d2")

    depends_on("r", type=("build", "run"))
    depends_on("perl", type=("build", "run"))
    depends_on("python", type=("build", "run"))
    depends_on("bowtie")
    depends_on("bowtie2")
    depends_on("star")

    def install(self, spec, prefix):
        make("install", "DESTDIR=%s" % prefix, "prefix=")