Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.

Peter van Heusden
I'm trying to use HISAT2 using a Docker-ized Galaxy (bgruening/galaxy-rna-seq:dev - Galaxy 17.05). I installed the HISAT2 index builder from the toolshed and built an index for the dm3 genome (resulting in an index in /galaxy-central/tool-data/dm3/hisat2_index/dm3). When I try and run HISAT2 with this newly created genome, I get the following error:

Traceback (most recent call last):
  File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
    job_wrapper.prepare()
  File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 878, in prepare
    tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
  File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 72, in set_compute_environment
    visit_input_values(self.tool.inputs, incoming, validate_inputs)
  File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 106, in visit_input_values
    visit_input_values(input.cases[values['__current_case__']].inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload)
  File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 112, in visit_input_values
    callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context)
  File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 77, in callback_helper
    new_value = callback(**args)
  File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 70, in validate_inputs
    value = input.from_json(value, request_context, context)
  File "/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 858, in from_json
    raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name)
ValueError: Parameter index requires a value, but has no legal values defined.


The "index" parameter is the one used in selecting between the genome from the History and the built-in genome options. Curiously if I spend some time changing this selection before running the tool the HISAT2 run completes successfully. This looks like a bug though - any workarounds or suggestions?

Thanks!
Peter

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/