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Unbound variable 'input'. in picrust2 pipeline #6655

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bgruening opened this issue Jan 5, 2025 · 1 comment
Open

Unbound variable 'input'. in picrust2 pipeline #6655

bgruening opened this issue Jan 5, 2025 · 1 comment

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@bgruening
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Tool-ID: toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pipeline/picrust2_pipeline/2.5.3+galaxy0
Unbound variable 'input'.

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 177, in respond
NameMapper.NotFound: cannot find 'ext'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/jobs/runners/__init__.py", line 297, in prepare_job
    job_wrapper.prepare()
  File "/opt/galaxy/server/lib/galaxy/jobs/__init__.py", line 1260, in prepare
    ) = tool_evaluator.build()
        ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/tools/evaluation.py", line 588, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/opt/galaxy/server/lib/galaxy/tools/evaluation.py", line 98, in global_tool_logs
    raise e
  File "/opt/galaxy/server/lib/galaxy/tools/evaluation.py", line 94, in global_tool_logs
    return func()
           ^^^^^^
  File "/opt/galaxy/server/lib/galaxy/tools/evaluation.py", line 611, in _build_command_line
    command_line = fill_template(
                   ^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 115, in fill_template
    return fill_template(
           ^^^^^^^^^^^^^^
  [Previous line repeated 7 more times]
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 123, in fill_template
    raise first_exception or e
  File "/opt/galaxy/server/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1182, in unicodify
    value = str(value)
            ^^^^^^^^^^
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 159, in respond
  File "cheetah_DynamicallyCompiledCheetahTemplate_1735036622_509089_88039.py", line 87, in getVarCond
  File "/opt/galaxy/venv/lib/python3.11/site-packages/Cheetah/Template.py", line 1458, in varExists
    valueFromSearchList(self.searchList(),
  File "/opt/galaxy/server/lib/galaxy/tools/evaluation.py", line 223, in input
    raise InputNotFoundSyntaxError(
galaxy.util.template.InputNotFoundSyntaxError: Unbound variable 'input'.
@bernt-matthias
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Is the a history tust can ne shared?

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@bgruening @bernt-matthias