# Copyright 2013-2022 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 RFgsea(RPackage):
    """Fast Gene Set Enrichment Analysis.

       The package implements an algorithm for fast gene set enrichment
       analysis. Using the fast algorithm allows to make more permutations and
       get more fine grained p-values, which allows to use accurate stantard
       approaches to multiple hypothesis correction."""

    bioc = "fgsea"

    version('1.22.0', commit='e4e203aa64faa984e0406fed5d87a422d9df92f2')
    version('1.20.0', commit='b704f81687dc16afdaafc6d30108c62a067856b2')
    version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318')
    version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
    version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b')
    version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d')
    version('1.4.1', commit='73de5ff364e520ac99507a9ee5a61a0d23d3c44e')
    version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')

    depends_on('r@3.3:', type=('build', 'run'))
    depends_on('r-rcpp', type=('build', 'run'))
    depends_on('r-data-table', type=('build', 'run'))
    depends_on('r-biocparallel', type=('build', 'run'))
    depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
    depends_on('r-gridextra', type=('build', 'run'))
    depends_on('r-fastmatch', type=('build', 'run'))
    depends_on('r-matrix', type=('build', 'run'), when='@1.6.0:')
    depends_on('r-bh', type=('build', 'run'), when='@1.10.1:')