Failing tools from week 33

[kjetilkl]

The following tools failed in week 33 due to problems with the tools themselves that we should address:

• NCBI BLAST+ makeblastdb (Galaxy Version 2.10.1+galaxy0)
  ID: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/2.10.1+galaxy0
  ERROR:

  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/5edc472ec434/ncbi_blast_plus/tools/ncbi_blast_plus/check_no_duplicates.py", line 41, in 
    for line in handle:
NameError: name 'handle' is not defined

• featureCounts (NeLS) (Galaxy version 1.6.4+NeLS)
  ID: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/kjetil/featurecounts/featurecounts/1.6.4+NeLS
  ERROR:

  File "/srv/galaxy/server/lib/galaxy/util/template.py", line 80, in fill_template
    return unicodify(t, log_exception=False)
  File "/srv/galaxy/server/lib/galaxy/util/__init__.py", line 1060, in unicodify
    value = str(value)
  File "/srv/galaxy/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1660746803_149984_28568.py", line 122, in respond
TypeError: 'filter' object is not subscriptable

COMMENT: This affects the first "GFF/GTF source" option, but the tool itself works if the user selects the equivalent third option. The same problem may also affect the tool called featureCounts (by kjetil). I'm not sure what the difference is between these two installations.
TODO: Fix the wrapper in the toolshed and install new revision. Review the other featureCounts tool also.

• Deseq (Galaxy version 1.0.0) (actually this is Deseq2!)
  ID: toolshed_nels/kjetil/deseq2/deseq_wrapper_script+1 1.0.0
  ERROR: tool_script.sh: Rscript: not found
  COMMENT: The wrapper does not specify any <requirements>. Perhaps "bioconductor-deseq2==1.34.0" will work. Also, there is a structure-problem with the XML-wrapper: the <citations> tag should not be inside <help>.
  TODO: Fix the tool wrapper in the toolshed (add requirements and move citations), install revision and build the container properly. Or: uninstall this tool and just use the "UiT DESeq2 wrapper", which looks like it could be the very same tool.

• Flye assembly (Galaxy version 2.8.1)
  ID: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/hien/flye_cigene/flye_cigene/2.8.1
  ERROR:

  File "/srv/galaxy/server/lib/galaxy/jobs/runners/__init__.py", line 243, in prepare_job
    job_wrapper.prepare()
  File "/srv/galaxy/server/lib/galaxy/jobs/__init__.py", line 1161, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/srv/galaxy/server/lib/galaxy/tools/evaluation.py", line 462, in build
    raise e
  File "/srv/galaxy/server/lib/galaxy/tools/evaluation.py", line 458, in build
    self.__build_command_line()
  File "/srv/galaxy/server/lib/galaxy/tools/evaluation.py", line 483, in __build_command_line
    command_line = fill_template(command, context=param_dict, python_template_version=self.tool.python_template_version)
  File "/srv/galaxy/server/lib/galaxy/util/template.py", line 107, in fill_template
    raise first_exception or e
  File "/srv/galaxy/server/lib/galaxy/util/template.py", line 80, in fill_template
    return unicodify(t, log_exception=False)
  File "/srv/galaxy/server/lib/galaxy/util/__init__.py", line 1060, in unicodify
    value = str(value)
  File "/srv/galaxy/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1661013088_7624614_98995.py", line 104, in respond
NameMapper.NotFound: cannot find 'ext'

In addition, the Minimap2 tool has failed a few times with "Segmentation fault", but it has worked fine on other occasions. And quite many runs of MAFFT ended with complaints that it could not rename a file (which did not exist), but I suspect that might be the user's own fault.