Installation errors

[ellasiera]

Very excited to give Rolypoly a try!
I'm trying to install it on a Linux cluster with the quick setup. During the installation I get this warning twice:

Supported shells are {bash, zsh, csh, posix, xonsh, cmd.exe, powershell, fish, nu}.
critical libmamba Shell not initialized
2026-03-12 16:19:23 Installing rolypoly-tk from PyPI

and this one:
Try 'rolypoly -h' for help
╭─ Error
│ No such command 'prepare-data'. │
╰──

But in the end it says the installation is complete.

Then I activate the Conda environment and run roly-poly --help, and get these errors:
Error loading command 'annotate': No module named 'typing_extensions'
Warning: Failed to load command 'annotate': No module named 'typing_extensions'
Error loading command 'annotate-prot': No module named 'typing_extensions'
Warning: Failed to load command 'annotate-prot': No module named 'typing_extensions'
Error loading command 'annotate-rna': No module named 'typing_extensions'
Warning: Failed to load command 'annotate-rna': No module named 'typing_extensions'
Error loading command 'assemble': No module named 'typing_extensions'
Warning: Failed to load command 'assemble': No module named 'typing_extensions'
Error loading command 'filter-contigs': No module named 'typing_extensions'
Warning: Failed to load command 'filter-contigs': No module named 'typing_extensions'
Error loading command 'filter-reads': No module named 'typing_extensions'
Warning: Failed to load command 'filter-reads': No module named 'typing_extensions'
Error loading command 'marker-search': No module named 'typing_extensions'
Warning: Failed to load command 'marker-search': No module named 'typing_extensions'
Error loading command 'rdrp-motif-search': No module named 'typing_extensions'
Warning: Failed to load command 'rdrp-motif-search': No module named 'typing_extensions'

Also, I would mention in the setup description on GitHub that this is Conda (or mamba) based. It's actually a good thing. I'd also include naming the environment as part of the installation.

Thanks for developing rolypoly!

[UriNeri]

Woops! the command internally was renamed to from prepare-data to get-data
the typing_extensions warnings should be fixes by 95b0316

I'll patch that today and ping here when done :)

[UriNeri]

@ellasiera ok the latest version on pypi, and the quick_setup.sh should be working now, lmk if you any issues!

[ellasiera]

The installation runs smoothly now, so naturally I ran into a bug while testing rolypoly on known RNA virus vOTUs. I wasn't sure whether this is still related to the installation or it's a separate issue. Here's the code and error:

rolypoly rdrp-motif-search -i Gary_RdRp_score70_verified_RdRp_mmseqs_vOTUs_linear.fasta -o rolypoly_test_out
Traceback (most recent call last):
File "/home/ellas/miniforge3/envs/rolypoly/bin/rolypoly", line 7, in
sys.exit(rolypoly())
^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rich_click/rich_command.py", line 402, in call
return super().call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1485, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rich_click/rich_command.py", line 216, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1873, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 824, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rolypoly/commands/identify_virus/rdrp_motif_search.py", line 247, in rdrp_motif_search
config = RdRpMotifSearchConfig(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rolypoly/commands/identify_virus/rdrp_motif_search.py", line 75, in init
Path(self.data_dir) / "profiles" / "motif_metadata.json"
^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/pathlib.py", line 1162, in init
super().init(*args)
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/pathlib.py", line 373, in init
raise TypeError(
TypeError: argument should be a str or an os.PathLike object where fspath returns a str, not 'NoneType'

Gary_RdRp_score70_verified_RdRp_mmseqs_vOTUs_linear.fasta is a nucleotide fasta file. I made sure the headers didn't have any special characters except _ and - and I linearized the sequences just in case. I changed the suffix to txt and uploaded it so you can try it yourself.

Gary_RdRp_score70_verified_RdRp_mmseqs_vOTUs_linear.txt

[ellasiera]

Also when I try to run run-pipeline that command doesn't work:
rolypoly run-pipeline -h

Usage: rolypoly [OPTIONS] COMMAND [ARGS]...

Try 'rolypoly -h' for help
╭─ Error ──────────────────╮
│ No such command 'run-pipeline'. │
╰──────────────────────╯

[UriNeri]

run-pipeline is actually called roll, I'll fix that naming error soon. Could you maybe share the log files from running the quick_setup.sh? or the contents of the rpconfig.json (in src/rolypoly/rpconfig.json) ?

[UriNeri]

Also, when you reran the installation script, did you first removed any created folders or environments made by the first faulty script? There's a rpconfig.json file that gets updated during install with the path to where the data is fetched to, but I'm not sure what would happen if it's already present. You could also try to modify that file directly and set the data path (ROLYPOLY_DATA) manually

[ellasiera]

My bad, clearing all files and reinstalling did the trick. rolypoly roll works, and since I already did the assemblies I'm currently trying the modules one by one. Thanks for your help!

[ellasiera]

Still getting an error for the motif search module though:
(rolypoly) [ellas@fe-open-01 tools]$ rolypoly rdrp-motif-search -i Gary_RdRp_score70_verified_RdRp_mmseqs_vOTUs_linear.fasta
Traceback (most recent call last):
File "/home/ellas/miniforge3/envs/rolypoly/bin/rolypoly", line 7, in
sys.exit(rolypoly())
^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rich_click/rich_command.py", line 402, in call
return super().call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1485, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rich_click/rich_command.py", line 216, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1873, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/click/core.py", line 824, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rolypoly/commands/identify_virus/rdrp_motif_search.py", line 247, in rdrp_motif_search
config = RdRpMotifSearchConfig(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/site-packages/rolypoly/commands/identify_virus/rdrp_motif_search.py", line 75, in init
Path(self.data_dir) / "profiles" / "motif_metadata.json"
^^^^^^^^^^^^^^^^^^^
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/pathlib.py", line 1162, in init
super().init(*args)
File "/home/ellas/miniforge3/envs/rolypoly/lib/python3.12/pathlib.py", line 373, in init
raise TypeError(
TypeError: argument should be a str or an os.PathLike object where fspath returns a str, not 'NoneType'

[dimitris-karapliafis]

Hi Ella,

The rdrp-motif-search module is still under development. Thanks for the feedback!
I tried to replicate the error, but on my machine it seems to work.
Could you share the .log and .rpconfig files to help us pinpoint the issue? Thanks!