| Previous changeset 9:1ac663f6a344 (2024-08-12) Next changeset 11:aa5586d83ae3 (2024-08-13) |
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Commit message:
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit effd27b9070dc4564d3cea38869d3bf043201683 |
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modified:
macros.xml run_lastz_tarball.py |
| b |
| diff -r 1ac663f6a344 -r d10e7502aba8 macros.xml --- a/macros.xml Mon Aug 12 15:41:05 2024 +0000 +++ b/macros.xml Tue Aug 13 15:56:46 2024 +0000 |
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| @@ -6,7 +6,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">1.04.22</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.05</token> <xml name="citations"> <citations> |
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| diff -r 1ac663f6a344 -r d10e7502aba8 run_lastz_tarball.py --- a/run_lastz_tarball.py Mon Aug 12 15:41:05 2024 +0000 +++ b/run_lastz_tarball.py Tue Aug 13 15:56:46 2024 +0000 |
| [ |
| @@ -34,6 +34,13 @@ ) -> None: os.chdir("galaxy/files") + # These are not considered errors even though + # we will end up with a segmented alignment + truncation_regex = re.compile( + r"truncating alignment (ending|starting) at \(\d+,\d+\); anchor at \(\d+,\d+\)$" + ) + truncation_msg = "truncation can be reduced by using --allocate:traceback to increase traceback memory" + while True: command_dict = input_queue.get() @@ -80,7 +87,6 @@ output_queue.put(elapsed) elif p.returncode == 1: - # should be more robust traceback_warning = True stderr_file = command_dict["stderr"] @@ -89,12 +95,11 @@ 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: + if ( + not truncation_regex.match(stderr_line) + and stderr_line != truncation_msg + ): traceback_warning = False if traceback_warning: @@ -229,9 +234,7 @@ format_name = f.readline() format_name = format_name.rstrip("\n") except FileNotFoundError: - sys.exit( - f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}" - ) + sys.exit(f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}") if format_name in ["bam", "maf"]: self.format_name = format_name |