ToolTemplatingException: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy3

[galaxyproject-sentryintegration]

Sentry Issue: GALAXY-MAIN-ZGC

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file'
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

NotFound: cannot find 'invert_targets_file' while searching for 'section.targets.invert_targets_file'
(12 additional frame(s) were not displayed)
...
  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_DynamicallyCompiledCheetahTemplate_1721670438_1896486_46576.py", line 333, in respond

ToolTemplatingException: Error occurred while building command line for tool 'toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy3'
  File "galaxy/jobs/runners/__init__.py", line 297, in prepare_job
    job_wrapper.prepare()
  File "galaxy/jobs/__init__.py", line 1260, in prepare
    ) = tool_evaluator.build()
  File "galaxy/tools/evaluation.py", line 611, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line", self.tool)
  File "galaxy/tools/evaluation.py", line 111, in global_tool_logs
    raise ToolTemplatingException(

(59406029) Failure preparing job

[jennaj]

Funny. I spent some time tracking this down, then found this!

Bug is triggered by a nested parameter: target chromosome filter

[galaxyproject-sentryintegration]

Another one, this time while accessing tgts_sec

Sentry Issue: GALAXY-MAIN-ZJ1

[mvdbeek]

The relevant part of the compiled template is this:

#set $section = $sec_consensus_variant_calling.variant_calling
#set $targets_path = None
#if $section.method == 'multiallelic':
    #if $section.genotypes.constrain == 'alleles':
        #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
        

#set $targets_path = None
#if 'targets' in $section
  #if $section.targets.targets_src == 'targets_file':
    #set $targets_path = 'targets_file.tab.gz'
    bgzip -c "$section.targets.targets_file" > $targets_path &&
    tabix -s 1 -b 2 -e 2 $targets_path &&
  #end if
#elif $tgts_sec.targets_file:
  #set $targets_path = 'targets_file.tab.gz'
  bgzip -c "$section.targets_file" > $targets_path &&
  tabix -s 1 -b 2 -e 2 $targets_path &&
#end if

where we set the targets_path variable.

Then later in the template we do:

#if $targets_path is not None:
  --targets-file "${section.invert_targets_file}${targets_path}"
#elif $section.targets_file:
  --targets-file "${section.invert_targets_file}${section.targets_file}"
#end if

invert_targets_file is never defined in the tool parameters. I guess we're missing the invert_targets_file boolean in sec_consensus_variant_calling.variant_calling