https://github.com/galaxyproject/galaxy
Tip revision: a8abf0e4b6196bd4acb38804ae799155bc4af900 authored by Dannon Baker on 23 February 2015, 16:25:45 UTC
Clone .gitignore
Clone .gitignore
Tip revision: a8abf0e
mine_wrapper.py
#!/usr/bin/env python
#Dan Blankenberg
"""
A wrapper script for running the MINE.jar commands.
"""
import sys, optparse, os, tempfile, subprocess, shutil
CHUNK_SIZE = 2**20 #1mb
BASE_NAME = "galaxy_mime_file.txt"
JOB_ID = "galaxy_mine"
def cleanup_before_exit( tmp_dir ):
if tmp_dir and os.path.exists( tmp_dir ):
print os.listdir( tmp_dir )
shutil.rmtree( tmp_dir )
def open_file_from_option( filename, mode = 'rb' ):
if filename:
return open( filename, mode = mode )
return None
def __main__():
#Parse Command Line
parser = optparse.OptionParser()
parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
(options, args) = parser.parse_args()
tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
if options.permute:
permute = "-permute"
else:
permute = ""
os.symlink( options.infile, tmp_input_name )
cmd = 'java -jar "%s" "%s" %s -cv%s -exp%s -c%s %s "%s"' % ( options.jar, tmp_input_name, options.master_variable, options.cv, options.exp, options.c, permute, JOB_ID )
print cmd
#set up stdout and stderr output options
stdout = open_file_from_option( options.stdout, mode = 'wb' )
stderr = open_file_from_option( options.stderr, mode = 'wb' )
#if no stderr file is specified, we'll use our own
if stderr is None:
stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
return_code = proc.wait()
if return_code:
stderr_target = sys.stderr
else:
stderr_target = sys.stdout
stderr.flush()
stderr.seek(0)
while True:
chunk = stderr.read( CHUNK_SIZE )
if chunk:
stderr_target.write( chunk )
else:
break
stderr.close()
print os.listdir( tmp_dir )
shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
cleanup_before_exit( tmp_dir )
if __name__=="__main__": __main__()