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('..')