def main():
usage = 'usage: %prog [options] arg'
parser = OptionParser(usage)
parser.add_option('-r', dest='restart', default=False, action='store_true', help='Do not overwrite existing files, as if restarting an aborted installation [Default: %default]')
parser.add_option('-w', dest='warn_on_error', default=False, action='store_true', help='Print a warning, rather than exit, if a dependency cannot be installed [Default: %default]')
(options,args) = parser.parse_args()
os.chdir('data')
############################################################
# download pre-trained model
############################################################
os.chdir('models')
if not options.restart or not os.path.isfile('pretrained_model.th'):
message('Downloading pre-trained model.')
cmd = 'wget https://www.dropbox.com/s/rguytuztemctkf8/pretrained_model.th.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
cmd = 'gunzip pretrained_model.th.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('..')
############################################################
# download human genome
############################################################
os.chdir('genomes')
if not options.restart or not os.path.isfile('hg19.fa'):
message('Downloading hg19 FASTA from UCSC. If you already have it, CTL-C to place a sym link in the genomes directory named hg19.fa')
# download hg19
cmd = 'wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz -O chromFa.tar.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# un-tar
cmd = 'tar -xzvf chromFa.tar.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# cat
cmd = 'cat chr?.fa chr??.fa > hg19.fa'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# clean up
os.remove('chromFa.tar.gz')
for chrom_fa in glob.glob('chr*.fa'):
os.remove(chrom_fa)
if not options.restart or not os.path.isfile('hg19.fa.fai'):
cmd = 'samtools faidx hg19.fa'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('..')
############################################################
# download and prepare public data
############################################################
if not options.restart or not os.path.isfile('encode_roadmap.h5'):
message('Downloading and preparing public data')
cmd = 'wget https://www.dropbox.com/s/h1cqokbr8vjj5wc/encode_roadmap.bed.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
cmd = 'gunzip encode_roadmap.bed.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
cmd = 'wget https://www.dropbox.com/s/8g3kc0ai9ir5d15/encode_roadmap_act.txt.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
cmd = 'gunzip encode_roadmap_act.txt.gz'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
'''
# download and arrange available data
cmd = './get_dnase.sh'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
# preprocess
cmd = 'preprocess_features.py -y -m 200 -s 600 -o encode_roadmap -c human.hg19.genome sample_beds.txt'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
'''
# make a FASTA file
cmd = 'bedtools getfasta -fi genomes/hg19.fa -bed encode_roadmap.bed -s -fo encode_roadmap.fa'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
# make an HDF5 file
cmd = 'seq_hdf5.py -c -r -t 71886 -v 70000 encode_roadmap.fa encode_roadmap_act.txt encode_roadmap.h5'
if subprocess.call(cmd, shell=True) and not options.warn_on_error: sys.exit(1)
def main():
usage = 'usage: %prog [options] arg'
parser = OptionParser(usage)
parser.add_option('--no-cuda', dest='no_cuda', default=False, action='store_true', help='Do not install packages only required for CUDA')
parser.add_option('-w', dest='warn_on_error', default=False, action='store_true', help='Print a warning, rather than exit, if a dependency cannot be installed [Default: %default]')
(options,args) = parser.parse_args()
# confirm luarocks
message('Checking for luarocks')
luarocks_which = subprocess.check_output('which luarocks', shell=True)
if luarocks_which == '':
message('Please install Torch7 first', 'error')
############################################################
# luarocks database
############################################################
# install luafilesystem
message('Installing luafilesystem')
cmd = 'luarocks install luafilesystem'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# install dpnn
message('Installing dpnn')
cmd = 'luarocks install dpnn'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# install inn
if not options.no_cuda:
message('Installing inn')
cmd = 'luarocks install inn'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
############################################################
# luarocks from github
############################################################
os.chdir('src')
# install torch-hdf5
cmd = 'git clone https://github.com/deepmind/torch-hdf5.git'
message('Installing torch-hdf5')
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('torch-hdf5')
cmd = 'luarocks make'
message('Installing make')
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('..')
os.chdir('..')
def main():
usage = 'usage: %prog [options] arg'
parser = OptionParser(usage)
parser.add_option('--no-cuda',
dest='no_cuda',
default=False,
action='store_true',
help='Do not install packages only required for CUDA')
parser.add_option(
'-w',
dest='warn_on_error',
default=False,
action='store_true',
help=
'Print a warning, rather than exit, if a dependency cannot be installed [Default: %default]'
)
(options, args) = parser.parse_args()
# confirm luarocks
message('Checking for luarocks')
luarocks_which = subprocess.check_output('which luarocks', shell=True)
if luarocks_which == '':
message('Please install Torch7 first', 'error')
############################################################
# luarocks database
############################################################
# install luafilesystem
message('Installing luafilesystem')
cmd = 'luarocks install luafilesystem'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# install dpnn
message('Installing dpnn')
cmd = 'luarocks install dpnn'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
# install inn
if not options.no_cuda:
message('Installing inn')
cmd = 'luarocks install inn'
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
############################################################
# luarocks from github
############################################################
os.chdir('src')
# install torch-hdf5
cmd = 'git clone https://github.com/deepmind/torch-hdf5.git'
message('Installing torch-hdf5')
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('torch-hdf5')
cmd = 'luarocks make'
message('Installing make')
if subprocess.call(cmd, shell=True) and not options.warn_on_error:
sys.exit(1)
os.chdir('..')
os.chdir('..')
