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issue registering command line arguments #26

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mkiyer opened this issue Dec 26, 2023 · 0 comments
Open

issue registering command line arguments #26

mkiyer opened this issue Dec 26, 2023 · 0 comments

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@mkiyer
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mkiyer commented Dec 26, 2023

I used bioconda to install snakemake 8.0.1

and then installed snakemake-storage-plugin-ftp

Now if I type "snakemake" I get the following error:

$ snakemake
Traceback (most recent call last):
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake/cli.py", line 2045, in main
parser, args = parse_args(argv)
^^^^^^^^^^^^^^^^
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake/cli.py", line 1637, in parse_args
parser = get_argument_parser()
^^^^^^^^^^^^^^^^^^^^^
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake/cli.py", line 1620, in get_argument_parser
StoragePluginRegistry().register_cli_args(parser)
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake_interface_common/plugin_registry/init.py", line 60, in register_cli_args
plugin.register_cli_args(argparser)
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake_interface_common/plugin_registry/plugin.py", line 152, in register_cli_args
settings.add_argument(*args, **kwargs)
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/snakemake/common/argparse.py", line 32, in add_argument
super().add_argument(*args, **kwargs)
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/site-packages/configargparse.py", line 1399, in add_argument
action = self.original_add_argument_method(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hpc/group/peterallen/mki3/sw/miniforge3/envs/smk/lib/python3.12/argparse.py", line 1472, in add_argument
action = action_class(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^
TypeError: _StoreTrueAction.init() got an unexpected keyword argument 'metavar'

I think there is some issue with adding plugins. Command line arguments need to be registered and there is a "store_true" command line argument that breaks the registration because "metavar" shouldn't be used. I'm not sure. Please help as I would love to upgrade to the next version of snakemake

https://stackoverflow.com/questions/11999416/python-argparse-metavar-and-action-store-true-together

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