Mercurial > repos > richard-burhans > batched_lastz

comparison run_lastz_tarball.py @ 8:3a67d287d19f draft

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planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit a5a11ffe6ec0c36c5997499a50d58c38c36d54ec
author richard-burhans
date Fri, 09 Aug 2024 21:10:40 +0000
parents 4cd7884635c2
children d10e7502aba8
comparison
equal deleted inserted replaced
7:4cd7884635c2 8:3a67d287d19f
38 command_dict = input_queue.get() 38 command_dict = input_queue.get()
39 39
40 if not command_dict: 40 if not command_dict:
41 return 41 return
42 42
43 args = ["lastz"] 43 args = ["lastz", "--allocate:traceback=1.99G"]
44 args.extend(command_dict["args"]) 44 args.extend(command_dict["args"])
45 45
46 stdin = command_dict["stdin"] 46 stdin = command_dict["stdin"]
47 if stdin is not None: 47 if stdin is not None:
48 stdin = open(stdin, "r") 48 stdin = open(stdin, "r")
60 60
61 for var in [stdin, stdout, stderr]: 61 for var in [stdin, stdout, stderr]:
62 if var is not None: 62 if var is not None:
63 var.close() 63 var.close()
64 64
65 if p.returncode != 0: 65 if p.returncode == 0:
66 sys.exit(f"command failed: {' '.join(args)}")
67 else:
68 stderr = command_dict["stderr"] 66 stderr = command_dict["stderr"]
69 if stderr is not None: 67 if stderr is not None:
70 try: 68 try:
71 statinfo = os.stat(stderr, follow_symlinks=False) 69 statinfo = os.stat(stderr, follow_symlinks=False)
72 except Exception: 70 except Exception:
78 if statinfo.st_size != 0: 76 if statinfo.st_size != 0:
79 sys.exit(f"stderr file is not empty: {' '.join(args)}") 77 sys.exit(f"stderr file is not empty: {' '.join(args)}")
80 78
81 elapsed = time.perf_counter() - begin 79 elapsed = time.perf_counter() - begin
82 output_queue.put(elapsed) 80 output_queue.put(elapsed)
81
82 elif p.returncode == 1:
83 # should be more robust
84 traceback_warning = True
85
86 stderr_file = command_dict["stderr"]
87 if stderr_file is None:
88 traceback_warning = False
89 else:
90 with open(stderr_file) as f:
91 for stderr_line in f:
92 for prefix in ["truncating alignment", "truncation can be reduced"]:
93 if stderr_line.startswith(prefix):
94 continue
95
96 stderr_line = stderr_line.strip()
97 if stderr_line:
98 traceback_warning = False
99
100 if traceback_warning:
101 elapsed = time.perf_counter() - begin
102 output_queue.put(elapsed)
103 else:
104 sys.exit(f"command failed: {' '.join(args)}")
105
106 else:
107 sys.exit(f"command failed: {' '.join(args)}")
83 108
84 if debug: 109 if debug:
85 print(f"runtime {elapsed}", file=sys.stderr, flush=True) 110 print(f"runtime {elapsed}", file=sys.stderr, flush=True)
86 111
87 112