Command line interface?

Question

Command line interface?

tseemann opened this issue 4 years ago · comments

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

Gerry Tonkin-Hill · Answer 1 · Wed Mar 18 2020 20:25:46 GMT+0800 (China Standard Time)

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

Gerry Tonkin-Hill · Answer 2 · Thu Mar 26 2020 03:03:37 GMT+0800 (China Standard Time)

I have added a command line script in 37435c2. 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.

Gerry Tonkin-Hill · Answer 3 · Thu Mar 26 2020 22:31:40 GMT+0800 (China Standard Time)

This is now included in the bioconda recipe.

Torsten Seemann · Answer 4 · Sat Mar 28 2020 05:24:57 GMT+0800 (China Standard Time)

@gtonkinhill thanks so much!

John Lees · Answer 5 · Mon Apr 27 2020 22:30:16 GMT+0800 (China Standard Time)

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

John Lees · Answer 6 · Tue Apr 28 2020 19:24:46 GMT+0800 (China Standard Time)

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

Gerry Tonkin-Hill · Answer 7 · Tue Jul 14 2020 07:57:24 GMT+0800 (China Standard Time)

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