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Add ability to set library path via COMPLEASM_LIBRARY_PATH if --library_path unspecified

Open douglasgscofield opened this issue 10 months ago • 1 comments

Adds the ability to specify the library path (what is set via --library_path) using the environment variable COMPLEASM_LIBRARY_PATH. The logic is:

  1. change default for --library_path options wherever they appear to None
  2. at the end of argument processing, if args.library_path == None, then check if environment variable COMPLEASM_LIBRARY_PATH is set
  3. if it is set, use its value for args.library_path
  4. if it is not set, use the current default value, mb_downloads, which will be in the current directory

This also modifies the __init__ logic in Downloader to do the same.

This change enables using a central location for lineage sets, useful for streamlining project-wide storage or, for example, for HPC clusters such as ours where we've already downloaded the lineage sets to the same system-wide location for both BUSCO and compleasm. These lineage sets do not often change, so enabling the use of a common location for them is not just feasible but recommended.

douglasgscofield avatar Apr 03 '24 13:04 douglasgscofield