parameters to specify database locations

[nick-youngblut]

Is your feature request related to a problem? Please describe.

For a number of reasons, software should generally be kept separate from large data files. The installation requires the placement of large data files into the gutSMASH codebase:

• gutsmash/antismash/databases
• gutsmash/antismash/detection/genefunctions/gut_data
• gutsmash/antismash/modules/clusterblast/data/known

It would be very helpful to provide the user with parameter to specify the locations of these database files, versus hard-coding the locations of the databases in the gutSMASH code.

Given the number of database files, it would also be helpful to provide bash (or similar) a script to help with downloading all of the files.

[nick-youngblut]

@victoriapascal can one use download_databases.py to download the required databases?

It's hard to tell what code actually functions for gutsmash versus just carry-over code due to forking from antismash.

[victoriapascal]

thanks @nick-youngblut for bringing this up. I realized this option is not available in gutsmash for now. Please, download the databases from here: https://gutsmash.bioinformatics.nl/download.html.