| Previous changeset 7:4cd7884635c2 (2024-07-30) Next changeset 9:1ac663f6a344 (2024-08-12) |
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Commit message:
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit a5a11ffe6ec0c36c5997499a50d58c38c36d54ec |
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modified:
run_lastz_tarball.py |
| b |
| diff -r 4cd7884635c2 -r 3a67d287d19f run_lastz_tarball.py --- a/run_lastz_tarball.py Tue Jul 30 19:53:53 2024 +0000 +++ b/run_lastz_tarball.py Fri Aug 09 21:10:40 2024 +0000 |
| [ |
| @@ -40,7 +40,7 @@ if not command_dict: return - args = ["lastz"] + args = ["lastz", "--allocate:traceback=1.99G"] args.extend(command_dict["args"]) stdin = command_dict["stdin"] @@ -62,9 +62,7 @@ if var is not None: var.close() - if p.returncode != 0: - sys.exit(f"command failed: {' '.join(args)}") - else: + if p.returncode == 0: stderr = command_dict["stderr"] if stderr is not None: try: @@ -81,6 +79,33 @@ elapsed = time.perf_counter() - begin output_queue.put(elapsed) + elif p.returncode == 1: + # should be more robust + traceback_warning = True + + stderr_file = command_dict["stderr"] + if stderr_file is None: + traceback_warning = False + else: + with open(stderr_file) as f: + for stderr_line in f: + for prefix in ["truncating alignment", "truncation can be reduced"]: + if stderr_line.startswith(prefix): + continue + + stderr_line = stderr_line.strip() + if stderr_line: + traceback_warning = False + + if traceback_warning: + elapsed = time.perf_counter() - begin + output_queue.put(elapsed) + else: + sys.exit(f"command failed: {' '.join(args)}") + + else: + sys.exit(f"command failed: {' '.join(args)}") + if debug: print(f"runtime {elapsed}", file=sys.stderr, flush=True) |