compleasm
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Add ability to set library path via COMPLEASM_LIBRARY_PATH if --library_path unspecified
Adds the ability to specify the library path (what is set via --library_path
) using the environment variable COMPLEASM_LIBRARY_PATH
. The logic is:
- change default for
--library_path
options wherever they appear toNone
- at the end of argument processing, if
args.library_path == None
, then check if environment variableCOMPLEASM_LIBRARY_PATH
is set - if it is set, use its value for
args.library_path
- 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.