import os
import platform
import subprocess
import sys

def create_env(dir_name):
    """creates virtenv with pip and python 2.7"""
    print >>sys.stderr, 'Make sure all requirements of INSTALL file are downloaded before running!!!'
    create_env = subprocess.call(['virtualenv','--distribute', dir_name,'--python=python2.7'])
    #assert: create_env == 0

def pip_install(dir_name):
    """pip install packages to virenv dir"""
    numpy = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'numpy'])
    if numpy != 0: raise Exception('can not download numpy READ REQUIREMENTS and TRY again!')
    processing = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'processing'])
    if processing != 0: raise Exception('can not download processing READ REQUIREMENTS and TRY again!')
    shapely = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'shapely==1.2.19'])
    if shapely != 0: raise Exception('can not download shapely READ REQUIREMENTS and TRY again!')
    pyfasta = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install','-Iv', 'pyfasta==0.4.5'])
    if pyfasta != 0: raise Exception('can not download pyfasta READ REQUIREMENTS and TRY again!')
    scipy = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'scipy'])
    if scipy != 0: raise Exception('can not download scipy READ REQUIREMENTS and TRY again!')
    Cython = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'Cython'])
    if Cython != 0: raise Exception('can not download Cython READ REQUIREMENTS and TRY again!')
    pyrex = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'Pyrex'])
    biopython = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'biopython'])
    if biopython != 0: raise Exception('can not download biopython READ REQUIREMENTS and TRY again!')
    pandas = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'pandas'])
    if pandas != 0: raise Exception('can not download pandas READ REQUIREMENTS and TRY again!')
    

def git_install(dir_name):
    """downloads git scripts to virenv bin"""
    print >>sys.stderr, 'Be patient, takes a long time to download'
    flatfeature = subprocess.call(['{0}/bin/pip'.format(dir_name), 'install', 'git+https://github.com/brentp/flatfeature.git'])
    if flatfeature != 0:
        raise Exception("Download git to contiune")
    quota = subprocess.Popen(['git', 'clone','https://github.com/tanghaibao/quota-alignment.git'],cwd=r'{0}/bin/'.format(dir_name)).wait()
    bcbb = subprocess.Popen(['git', 'clone', 'https://github.com/chapmanb/bcbb.git'],cwd=r'{0}/bin/'.format(dir_name)).wait()


def setup_install(dir_name):
    """installs setup install files to virenv directory"""
    subprocess.Popen(['../../python2.7','setup.py','install'],cwd=r'{0}/bin/bcbb/gff/'.format(dir_name)).wait()
    subprocess.Popen(['../../../../{0}/bin/python2.7'.format(dir_name),'setup.py','install'],cwd=r'pipeline/coann/brents_bpbio/biostuff/').wait()
    subprocess.Popen(['../../../../../{0}/bin/python2.7'.format(dir_name),'setup.py','install'],cwd=r'pipeline/coann/brents_bpbio/blasttools/blast_misc/').wait()
    subprocess.Popen(['../../../../../{0}/bin/python2.7'.format(dir_name),'setup.py','install'],cwd=r'pipeline/coann/brents_bpbio/scripts/bblast/').wait()
    co_anno = subprocess.Popen(['../../../../{0}/bin/python2.7'.format(dir_name),'setup.py','install'],cwd=r'pipeline/coann/brents_bpbio/co-anno/').wait()

def install_blast(dir_name):
    opersys = platform.system()
    if opersys == 'Darwin':
        link = 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/blast-2.2.26-universal-macosx.tar.gz'
    elif opersys == 'Linux':
        if '_32' in platform.version():
            link = 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/blast-2.2.26-ia32-linux.tar.gz'
        else:
            link = 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/blast-2.2.26-x64-linux.tar.gz'
    subprocess.Popen(['wget','-O','blast.tar.gz',link],cwd=r'{0}/bin/'.format(dir_name)).wait()
    subprocess.Popen(['tar', '-xvzf','blast.tar.gz'],cwd=r'{0}/bin/'.format(dir_name)).wait()

def install_lastz(dir_name):
    if "lastz-distrib" not in os.listdir(dir_name):
        link = 'http://www.bx.psu.edu/~rsharris/lastz/newer/lastz-1.03.02.tar.gz'
        subprocess.Popen(['wget','-O','lastz.tar.gz',link],cwd=r'{0}/bin/'.format(dir_name)).wait()
        subprocess.Popen(['tar', '-xvzf','lastz.tar.gz'],cwd=r'{0}/bin/'.format(dir_name)).wait()
    passed = subprocess.Popen(['make'],cwd=r'{0}/bin/lastz-distrib-1.03.02/'.format(dir_name)).wait()
    if passed != 0: print >>sys.stderr, 'Delete the word -Werror at the line 31 in cns_pipeline/bin/lastz-distrib-1.03.02/src/Makefile and re-run bootstrap.py!!!!!!'
    cwd = r'{0}/bin/lastz-distrib-1.03.02/'.format(dir_name)
    opts = 'LASTZ_INSTALL={0}/cns_pipeline/bin/'.format(os.getcwd())
    subprocess.Popen([opts,'make','install'],cwd=cwd, shell=True).wait()






create_env('cns_pipeline')
pip_install('cns_pipeline')
git_install('cns_pipeline')
setup_install('cns_pipeline')
install_blast('cns_pipeline')
install_lastz('cns_pipeline')