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Fix stringtie deseq2 output in mixed mode

Open mvdbeek opened this issue 1 year ago • 3 comments

Fixes https://sentry.galaxyproject.org/share/issue/d8a2554ecaab4c7582a17e0e1102b25a/::

NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond
NotFound: cannot find 'input_bam'
  File "galaxy/jobs/runners/pulsar.py", line 499, in __prepare_job
    job_wrapper.prepare(**prepare_kwds)
  File "galaxy/jobs/__init__.py", line 1260, in prepare
    ) = tool_evaluator.build()
  File "galaxy/tools/evaluation.py", line 588, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "galaxy/tools/evaluation.py", line 98, in global_tool_logs
    raise e
  File "galaxy/tools/evaluation.py", line 94, in global_tool_logs
    return func()
  File "galaxy/tools/evaluation.py", line 611, in _build_command_line
    command_line = fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 115, in fill_template
    return fill_template(
  File "galaxy/util/template.py", line 123, in fill_template
    raise first_exception or e
  File "galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "galaxy/util/__init__.py", line 1183, in unicodify
    value = str(value)
  File "Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1720636986_2572532_79544.py", line 272, in respond

IMO this tools should have been split into two tools when long reads / mixed read support was added. This would have made the command section a lot simpler. There's just way too many permutations one needs to test in the absence of type checking for cheetah code.

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  • [ ] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • [ ] License permits unrestricted use (educational + commercial)
  • [ ] This PR adds a new tool or tool collection
  • [ ] This PR updates an existing tool or tool collection
  • [ ] This PR does something else (explain below)

mvdbeek avatar Jul 11 '24 08:07 mvdbeek

Ran into this one again today.

mvdbeek avatar Sep 12 '24 13:09 mvdbeek

Sentry Issue: GALAXY-MAIN-ZJ7

galaxyproject-sentryintegration[bot] avatar Sep 12 '24 13:09 galaxyproject-sentryintegration[bot]

Ping @nsoranzo

bernt-matthias avatar Feb 06 '25 07:02 bernt-matthias