I would like to have a central place where things like reference alignments, taxonomies, etc… can be kept. It would be great if there was place to set a default search location for such things. I see a set.dir command that handles input and output but it would be nice if you had a search_path= or some such thing where MOTHUR would look if the specified file was not found in ./or the input directory. Bonus if it was configurable as an environment variable like $MOTHUR_FILES. This would allow my users to have a consistent set of references without remembering/typing long paths. Perhaps such a thing exists?
+1 on this idea
(insert URL for electronic cigarettes here)
Thanks for the suggestion, this will be part of version 1.12.0.
Thanks for the quick implementation. One minor point. When I try it, I get an error because the directory I supplied in tempdefault is not writable (it is a data directory off of root with permissions like: drwxr-xr-x). That was how I intended to set it up so the references did not get altered. As it stands I just used chmod to add write access. In a future version it would be nice if “writability” was not a requirement. Thanks!
Thanks for the suggestion. We are releasing a 1.12.2 later today to fix a few issues and will include this change.