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jbloomlab / SARS-CoV-2-RBD_DMS

Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike
BSD 3-Clause "New" or "Revised" License
43 stars 17 forks source link

install `dssp` into conda environment #4

Closed jbloom closed 4 years ago

jbloom commented 4 years ago

This is better than including the executable in the repo. It is now just installed with other programs and can be accessed with the command mkdssp (note not dssp).

jbloom commented 4 years ago

@tylernstarr, sorry, this should be the last trivial organizational one---then I'll start on the actual problem of handling multiple alignment targets. Can you just check and review this one?

jbloom commented 4 years ago

If you've activated the conda environment, I think you then just reference it with mkdssp without a full path as it should be in the executable path. Does this not work? Assuming it works, this is better because then the analysis can also be run in some other directory as it doesn't have a hard-coded path name.

tylernstarr commented 4 years ago

True, I guess I don’t know if R references the executable path or if it requires a full path. I’ll approve the change for now and test it out

jbloom commented 4 years ago

I think it references executable path. Look at example from the bio3d package: their default is just an executable path of dssp: http://thegrantlab.org/bio3d/html/dssp.html