# Copyright 2013-2019 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 import *
from os import symlink


class Rmats(Package):
    """MATS is a computational tool to detect differential alternative
       splicing events from RNA-Seq data."""

    homepage = "https://rnaseq-mats.sourceforge.net/index.html"
    url      = "https://downloads.sourceforge.net/project/rnaseq-mats/MATS/rMATS.4.0.2.tgz"

    version('4.0.2', sha256='afab002a9ae836d396909aede96318f6dab6e5818078246419dd563624bf26d1')

    depends_on('python@2.7:', type='run')
    depends_on('py-numpy', type=('build', 'run'))
    depends_on('openblas')

    def install(self, spec, prefix):
        # since the tool is a python script we install it to /usr/lib
        install_tree('rMATS-turbo-Linux-UCS4', join_path(prefix.lib, 'rmats'))

        # the script has an appropriate shebang so a quick symlink will do
        set_executable(join_path(prefix.lib, 'rmats/rmats.py'))
        mkdirp(prefix.bin)
        symlink(join_path(prefix.lib, 'rmats/rmats.py'),
                join_path(prefix.bin, 'rmats'))
