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Expand environmental variables in GTDBTK_DATA_PATH #486

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donovan-h-parks opened this issue Mar 14, 2023 · 1 comment
Closed

Expand environmental variables in GTDBTK_DATA_PATH #486

donovan-h-parks opened this issue Mar 14, 2023 · 1 comment
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enhancement Proposed feature or change to GTDB-Tk.

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@donovan-h-parks
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It appears GTDB-Tk currently treats the GTDBTK_DATA_PATH environmental variable as a string literal. This can be challenging in certain environments where the path to the GTDB-Tk reference database is best accessed via an environmental variable, e.g.:

GTDBTK_DATA_PATH =$ROOT_DB_PATH/gtdbtk/release207_v2

Can GTDB-Tk be modified so the $ROOT_DB_PATH environmental variable is expanded out. I believe this can be done with:

os.path.expandvars('$ROOT_DB_PATH/gtdbtk/release207_v2')
@donovan-h-parks donovan-h-parks added the enhancement Proposed feature or change to GTDB-Tk. label Mar 14, 2023
@pchaumeil
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available in https://github.com/Ecogenomics/GTDBTk/releases/tag/2.2.5

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@donovan-h-parks @pchaumeil