scores_path_temp = os.path.join(scores_path, 'Temp')
if os.path.isdir(scores_path_temp):
scores_path = scores_path_temp
scores_path_temp = os.path.join(scores_path, 'Temp')
if os.path.isdir(scores_path_temp):
scores_path = scores_path_temp
bzip_cmd = [ 'bzip2', '-9', '-c' ]
tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
tar_dest = open(tar_dest_name, 'w')
logging.info("Compressing score files from %s" % (scores_path,))
logging.info("Running tar: " + " ".join(tar_cmd[:10]))
logging.info("Running bzip2: " + " ".join(bzip_cmd))
bzip_cmd = [ 'bzip2', '-9', '-c' ]
tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
tar_dest = open(tar_dest_name, 'w')
logging.info("Compressing score files from %s" % (scores_path,))
logging.info("Running tar: " + " ".join(tar_cmd[:10]))
logging.info("Running bzip2: " + " ".join(bzip_cmd))
env = {'BZIP': '-9'}
tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, env=env,
env = {'BZIP': '-9'}
tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, env=env,
def compress_eland_results(gerald_object, cycle_dir):
"""
Compress eland result files into the archive directory
def compress_eland_results(gerald_object, cycle_dir):
"""
Compress eland result files into the archive directory
bzip.wait()
def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
bzip.wait()
def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
# compress eland result files
compress_eland_results(g, cycle_dir)
# build srf commands
lanes = range(1,9)
# compress eland result files
compress_eland_results(g, cycle_dir)
# build srf commands
lanes = range(1,9)
- srf_cmds = srf.make_commands(r.pathname, lanes, "woldlab", cycle_dir)
+ run_name = srf.pathname_to_run_name(r.pathname)
+ srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
def rm_list(files, dry_run=True):
srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
def rm_list(files, dry_run=True):