def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
infile = ""
tmpdir = ""
email = ""
jobid = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-tmpdir", "--tmpdir"]:
(tmpdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-jobid", "--jobid"]:
(jobid, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"]:
(g_params['base_www_url'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-email", "--email"]:
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = True
i += 1
elif argv[i] in ["-only-get-cache", "--only-get-cache"]:
g_params['isOnlyGetCache'] = True
i += 1
else:
print("Error! Wrong argument:", argv[i], file=sys.stderr)
return 1
else:
infile = argv[i]
i += 1
if jobid == "":
print("%s: jobid not set. exit" % (sys.argv[0]), file=sys.stderr)
return 1
g_params['jobid'] = jobid
# create a lock file in the resultpath when run_job.py is running for this
# job, so that daemon will not run on this folder
lockname = "runjob.lock"
lock_file = "%s/%s/%s" % (path_result, jobid, lockname)
g_params['lockfile'] = lock_file
fp = open(lock_file, 'w')
try:
fcntl.lockf(fp, fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
print("Another instance of %s is running" % (progname),
file=sys.stderr)
return 1
if myfunc.checkfile(infile, "infile") != 0:
return 1
if outpath == "":
print("outpath not set. exit", file=sys.stderr)
return 1
elif not os.path.exists(outpath):
try:
subprocess.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError as e:
print(e, file=sys.stderr)
return 1
if tmpdir == "":
print("tmpdir not set. exit", file=sys.stderr)
return 1
elif not os.path.exists(tmpdir):
try:
subprocess.check_output(["mkdir", "-p", tmpdir])
except subprocess.CalledProcessError as e:
print(e, file=sys.stderr)
return 1
numseq = myfunc.CountFastaSeq(infile)
g_params['debugfile'] = "%s/debug.log" % (outpath)
return RunJob(infile, outpath, tmpdir, email, jobid, g_params)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
infile = ""
tmpdir = ""
email = ""
jobid = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-apptype", "--apptype"]:
(g_params['app_type'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-tmpdir", "--tmpdir"]:
(tmpdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-jobid", "--jobid"]:
(jobid, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"]:
(g_params['base_www_url'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-email", "--email"]:
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = True
i += 1
elif argv[i] in ["-only-get-cache", "--only-get-cache"]:
g_params['isOnlyGetCache'] = True
i += 1
else:
print("Error! Wrong argument:", argv[i], file=sys.stderr)
return 1
else:
infile = argv[i]
i += 1
if jobid == "":
print("%s: jobid not set. exit" % (sys.argv[0]), file=sys.stderr)
return 1
if myfunc.checkfile(infile, "infile") != 0:
return 1
if outpath == "":
print("outpath not set. exit", file=sys.stderr)
return 1
elif not os.path.exists(outpath):
try:
os.makedirs(outpath)
except Exception as e:
print(e, file=sys.stderr)
return 1
if tmpdir == "":
print("tmpdir not set. exit", file=sys.stderr)
return 1
elif not os.path.exists(tmpdir):
try:
os.makedirs(tmpdir)
except Exception as e:
print(e, file=sys.stderr)
return 1
numseq = myfunc.CountFastaSeq(infile)
g_params['debugfile'] = "%s/debug.log" % (outpath)
if g_params['app_type'] == "SCAMPI-single":
return RunJob_single(infile, outpath, tmpdir, email, jobid, g_params)
else:
return RunJob_msa(infile, outpath, tmpdir, email, jobid, g_params)