# 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 Bowtie(MakefilePackage):
    """Bowtie is an ultrafast, memory-efficient short read aligner
    for short DNA sequences (reads) from next-gen sequencers."""

    homepage = "https://sourceforge.net/projects/bowtie-bio/"
    url      = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"

    version('1.3.0', sha256='d7c2d982a67884909f284a0ff150b56b20127cd7a1ced461c3c4c03e6a6374c5')
    version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
    # The bowtie project git tagged and GitHub released a v1.2.2,
    # discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
    # 1.2.2 release to use it rather than making a new `1.2.2_p1`
    # release.
    #
    # We point both of the Spack versions at the same tarball so they
    # build the binaries that are on the release page as v1.2.2
    version('1.2.2_p1', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1')
    version('1.2.2', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1', url="https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz")
    version('1.2.1.1', sha256='1b38408b88f61d18d7ff28b2470a8cfeefccb3fc59fd46e4cc62e23874e52c20')
    version('1.2.1', sha256='b2a7c8c879cb08f00a82665bee43e1d4861de44a87912c54d168e44c90869728')
    version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894')
    # Keeping the old 1.2 version around for reproducibility, it's not
    # clearly identical to 1.2.0.
    version('1.2', sha256='b1052de4253007890f6436e6361d40148bc2a5a9dd01827bb9f34097747e65f8', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')

    # 1.2.2 and 1.2.2_p1 fail to build with %gcc@8.3.0
    # with and without issue-87 patch
    conflicts('%gcc@8:', when='@1.2.2')
    conflicts('%gcc@8:', when='@1.2.2_p1')

    variant('tbb', default=False, description='Use Intel thread building block')

    depends_on('tbb', when='+tbb')
    depends_on('zlib')

    # See: https://github.com/BenLangmead/bowtie/issues/87, a
    # different fix is in the FreeBSD ports/package tree
    # https://svnweb.freebsd.org/ports?view=revision&revision=483954
    patch('issue-87.patch', when='@:1.2.2 %gcc@8.0.0:')

    # correspond to 'aarch64' architecture
    # reference: https://github.com/BenLangmead/bowtie/pull/13
    patch('for_aarch64.patch', when='@1.2.0:1.2 target=aarch64:')

    # measures for narrowing error
    patch('fix_narrowing_err.patch', when='@1.2.1:1.2.3')
    patch('fix_narrowing_err_1.3.0.patch', when='@1.3.0:')

    def edit(self, spec, prefix):
        makefile = FileFilter('Makefile')
        makefile.filter('CC = .*', 'CC = ' + env['CC'])
        makefile.filter('CXX = .*', 'CPP = ' + env['CXX'])

    def build(self, spec, prefix):
        if '+tbb' in spec:
            make()
        else:
            make('NO_TBB=1')

    def install(self, spec, prefix):
        make('prefix={0}'.format(self.prefix), 'install')