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.
(also at: https://gist.github.com/pvanheus/f463b4a60b064c6f45dd99c1bf883480)
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