Hi @Tabima! I looked through all of code and made some changes to the parts I understood. I dont know what the functions actually do well enough to comment on their results or anything like that, so all my changes should only effect things like OS compatibility and not the analyses themselves.
Lets meet up in person and go over things before merging if you want.
made file paths work on all OSes
MAFFT and HMMER paths now do not need to be specified by default, but still can be. Should work on all OSes by default if programs are in search path. Finding the path and complaining if not found is now in separate functions. mafft.path now accepts either the folder path or the path to the executable itself.
added template for package help page
used system2 instead of system since it is supposed to be more reliable across OSes
added seed option to hmm.search, but it did not completely fix the randomness
Tabima
commented
7 years ago
Hi @Tabima! I looked through all of code and made some changes to the parts I understood. I dont know what the functions actually do well enough to comment on their results or anything like that, so all my changes should only effect things like OS compatibility and not the analyses themselves.
Lets meet up in person and go over things before merging if you want.
mafft.pathnow accepts either the folder path or the path to the executable itself.system2instead ofsystemsince it is supposed to be more reliable across OSeshmm.search, but it did not completely fix the randomness