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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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umi_tools not working #594

Closed gevro closed 1 year ago

gevro commented 1 year ago

Hi, I tried installing with pip and also from the ZIP release. Both give me this error:

$ umi_tools dedup 'dedup' is not a UMI-tools command. See 'umi_tools -h'.

Also, the help is not showing: $ umi_tools dedup --help UMI-Tools: Version 1.1.4

Note: this is happening for every tool command.

I think something is broken in the current version.

TomSmithCGAT commented 1 year ago

OK, the error ('dedup' is not a UMI-tools command. See 'umi_tools -h') is odd and I cannot reproduce. E.g the following setup works fine after downloading ZIP release

conda create -n umi_tools_sandbox python=3.10
conda activate umi_tools_sandbox
pip install ~/Downloads/UMI-tools-1.1.4.zip
umi_tools dedup

The issue with the help text has been caught and is waiting on #586. Sorry about that one. For now, you'll need to refer to the online documentation.

gevro commented 1 year ago

Ok thanks. I managed to run umi_tools find on a different computing cluster. Not sure how the other error is happening.