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gtonkinhill / fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
MIT License
58 stars 8 forks source link

Command line interface? #11

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

Would it be possible to add a command line interface version of this tool?

gtonkinhill commented 4 years ago

I think this should be possible using Rscript. Would this suffice? It would still require installing fastbaps using R/conda.

gtonkinhill commented 4 years ago

I have added a command line script in 37435c2031524dd49dbbc8734eb193d485d3778b. It's located in the fastbaps/inst subdirectory. I will look at updating the conda recipe to put this in the users path. If I get a chance I'll see if I can get it setup in a docker instance as well.

gtonkinhill commented 4 years ago

This is now included in the bioconda recipe.

tseemann commented 4 years ago

@gtonkinhill thanks so much!

johnlees commented 4 years ago

I think optparse might need to be added to the dependency lists for this

johnlees commented 4 years ago

Also v. minor issue if reopening this, phylogeny is misspelled as 'phylogney' in the options

gtonkinhill commented 4 years ago

I'd forgotten about this but it should be fixed in the latest release.