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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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Check for the presence of an environment variable for location of databases #80

Closed linsalrob closed 1 year ago

linsalrob commented 2 years ago

Can we please define an environmental variable HECATOMB_DB that is checked for first?

If set, we should use this as the location of the databases and die with an appropriate error if the databases are not present in this location.

This would allow multiple users to access the database from a common location (this is similar to $KRAKEN2_DEFAULT_DB and $SUPERFOCUS_DB)

beardymcjohnface commented 1 year ago

Hecatomb will look for DB location in the following order:

config > environment variable HECATOMB_DB > default location