The fimo tool was removed from `tool_conf.xml.sample` in 2014
(commit fa11d10c8b) and migrated to the
tools-iuc repository since 2015
( https://github.com/galaxyproject/tools-iuc/pull/499 ).
This bundled version doesn't probably work any more and is not
available on the UseGalaxy.* servers.
This allows us to remove `galaxy-sequence-utils` from the project
dependencies, since the other 2 tools
(`lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml`
and `tools/maf/vcf_to_maf_customtrack.xml`) correctly specify it as a
requirement.
I think this fixes https://github.com/galaxyproject/galaxy/issues/18770
? I did manage to get the redirect to Galaxy, however the user interface
looks pretty weird to me, so I'm not sure this is how it is meant to be
?
We were passing 'false' to --export-metadata-files, but it was
considered True (non-zero length string), and the metadata was
always included in the export.
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
Error popping up all the time:
```
Traceback (most recent call last):
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
tool = self.create_tool(
^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
return create_tool_from_source(self.app, tool_source, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 820, in __init__
raise e
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 817, in __init__
self.parse(tool_source, guid=guid, dynamic=dynamic)
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1142, in parse
self.parse_inputs(self.tool_source)
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1427, in parse_inputs
inputs = self.parse_input_elem(page_source, enctypes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1622, in parse_input_elem
param = self.parse_param_elem(input_source, enctypes, context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1635, in parse_param_elem
param = ToolParameter.build(self, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 330, in build
return parameter_types[param_type](tool, input_source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 2071, in __init__
super().__init__(tool, input_source, trans)
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 1863, in __init__
super().__init__(tool, input_source)
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 186, in __init__
self.validators.append(validation.Validator.from_element(self, elem))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/validation.py", line 45, in from_element
return validator_types[_type].from_element(param, elem)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/validation.py", line 399, in from_element
assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
AssertionError: File /gpfs1/data/galaxy_server/galaxy/tool-data/sift_db.loc specified by the 'filename' attribute not found
```
I think using the other validator should not cause so much trouble.
Allows moving all data source tools using the script to profile 20.09.
For more recent profiles data_source.py would have to work outside of
Galaxy's Python environment.
- Drop support for very old format of specifying execution params in a
tabular file instead of a json one
- Use O_TRUNC to discard previous file contents instead of opening for
writing, then closing
- Do not silently ignore non-integer values for max_file_size
Nicola Soranzo