# Copyright 2013-2020 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 *


class Isescan(Package):
    """A python pipeline to identify IS (Insertion Sequence) elements in
       genome and metagenome"""

    homepage = "https://github.com/xiezhq/ISEScan"
    url      = "https://github.com/xiezhq/ISEScan/archive/v1.7.2.1.tar.gz"

    version('1.7.2.1', sha256='b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d')

    depends_on('python@3.3.3:', type='run')
    depends_on('py-numpy@1.8.0:', type='run')
    depends_on('py-scipy@0.13.1:', type='run')
    depends_on('py-biopython@1.62:', type='run')
    depends_on('py-fastcluster', type='run')
    depends_on('py-argparse', type='run')
    depends_on('blast-plus@2.2.31:', type='run')
    depends_on('fraggenescan@1.30:', type='run')
    depends_on('hmmer@3.1b2:', type='run')

    def setup_run_environment(self, env):
        env.prepend_path('PATH', self.prefix)
        env.prepend_path('LD_LIBRARY_PATH',
                         join_path(self.prefix, 'ssw201507'))

    def install(self, spec, prefix):
        # build bundled SSW library
        with working_dir('ssw201507'):
            Executable(spack_cc)(
                '-O3', '-pipe', self.compiler.cc_pic_flag, '-shared',
                '-rdynamic', '-o', 'libssw.' + dso_suffix, 'ssw.c', 'ssw.h',
            )

        # set paths to required programs
        blast_pfx = self.spec['blast-plus'].prefix.bin
        blastn_path = blast_pfx.blastn
        blastp_path = blast_pfx.blastp
        makeblastdb_path = blast_pfx.makeblastdb

        hmmer_pfx = self.spec['hmmer'].prefix.bin
        phmmer_path = hmmer_pfx.phmmer
        hmmsearch_path = hmmer_pfx.hmmsearch

        fgs_pfx = self.spec['fraggenescan'].prefix.bin
        fgs_path = join_path(fgs_pfx, 'run_FragGeneScan.pl')

        constants = FileFilter('constants.py')

        constants.filter('/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl',
                         fgs_path, string=True)
        constants.filter('/apps/inst/hmmer-3.3/bin/phmmer',
                         phmmer_path, string=True)
        constants.filter('/apps/inst/hmmer-3.3/bin/hmmsearch',
                         hmmsearch_path, string=True)
        constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastn',
                         blastn_path, string=True)
        constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastp',
                         blastp_path, string=True)
        constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb',
                         makeblastdb_path, string=True)

        # install the whole tree
        install_tree('.', prefix)
        set_executable(join_path(prefix, 'isescan.py'))
