logging.basicConfig(filename=logfile)
log = logging.getLogger(os.path.basename(tool))
hdfs = pydoop.hdfs.hdfs("default", 0)
log.debug("connected to hdfs at %s", hdfs.host)
# hack to read the input path directly from the command line
#input_paths = [ galaxy_input ]
with open(galaxy_input) as f:
input_paths = [s.rstrip("\n") for s in f.readlines()]
output_path = os.path.join(hdfs.working_directory(),
"galaxy-wrapper-%f" % random.random())
hdfs.close()
log.debug("hdfs closed")
log.debug("options: %s", options)
log.debug("input: %s", input_paths)
log.debug("output: %s", output_path)
with open(galaxy_output, 'w') as f:
f.write(output_path)
command = [tool]
command.extend(options)
command.extend(input_paths)
command.append(output_path)
try:
def close():
"""
Closes an the HDFS connection (disconnects to the namenode)
"""
hdfs.close()
logging.basicConfig(filename=logfile)
log = logging.getLogger(os.path.basename(tool))
hdfs = pydoop.hdfs.hdfs("default", 0)
log.debug("connected to hdfs at %s", hdfs.host)
# hack to read the input path directly from the command line
#input_paths = [ galaxy_input ]
with open(galaxy_input) as f:
input_paths = [ s.rstrip("\n") for s in f.readlines() ]
output_path = os.path.join( hdfs.working_directory(), "galaxy-wrapper-%f" % random.random())
hdfs.close()
log.debug("hdfs closed")
log.debug("options: %s", options)
log.debug("input: %s", input_paths)
log.debug("output: %s", output_path)
with open(galaxy_output, 'w') as f:
f.write(output_path)
command = [tool]
command.extend(options)
command.extend(input_paths)
command.append(output_path)
try:
