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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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removing unnecessary dependencies #120

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

@Hego-CCTB Currently, AMALGKIT installs these packages by default: 'numpy','pandas','biopython','lxml','nltk','obonet'. And I would like to minimize it before publication. I understand that nltk (obonet too?) were used in amalgkit metadata --tissue_detect, which did not work as well as we expected. We should keep the package dependencies if you are still using/developing this functionality, but they may be removed otherwise. Please let me know.

Hego-CCTB commented 1 year ago

Obonet nltk and all related code can be safely removed. I'll take care of that.

kfuku52 commented 1 year ago

I will take care of it.

kfuku52 commented 1 year ago

done