metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data
GNU General Public License v3.0
21 stars 12 forks source link

Use environment variable for db #70

Closed linsalrob closed 2 years ago

linsalrob commented 2 years ago

I added an option to set the database path using the environmental variable SUPERFOCUS_DB.

There are instances when we don't know a priori what the path is and so this allows users to set an environmental variable to define the path.

For example, if super-focus is included in a snakemake pipeline installed via conda, the user can install the databases somewhere and set the environment variable to point to the database location.

To use:

export SUPERFOCUS_DB=/path/to/database/location/

there is now no need to use the --alternate-directory flag.

metageni commented 2 years ago

Thanks @linsalrob