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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
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Phylo pipeline "unknown command" #48

Closed 974ben closed 1 year ago

974ben commented 1 year ago

Hello,

I am trying to run the phylo pipeline with the latest version of paleomix - 1.3.7

I've tried lots of variants on the same command, including using example documentation as well as my own own makefile, but consistently get the same error message:

ERROR unknown command 'genotyping'

Just one example of the commands yielding this error is: paleomix phylo_pipeline genotyping+msa+phylogeny makefile.yaml

I've checked and I believe I have all the correct development files installed. Could you advise what might be causing this error?

Many thanks, Ben

MikkelSchubert commented 1 year ago

Hi Ben,

Sorry for the trouble and thank you for the report!

It seems that I made a mistake while writing the documentation. Instead of genotyping it should be genotype, as in

 paleomix phylo_pipeline genotype+msa+phylogeny makefile.yaml

However, I have to caution that the phylo pipeline is deprecated and slated for removal in the next major release of paleomix (2.0) sometime in the future, due to lack of use and hence development. However, I'll gladly answer your questions and help with any issues you run into.

Best, Mikkel

MikkelSchubert commented 1 year ago

I've released a version of paleomix that fixes this (v1.3.8). Once again thank you for reporting this and do let me know if you run into any other issues.

Best, Mikkel