The Unipept metaproteomics and metagenomics pipelines operate on data found in the [Uniprot] database. This collection of scripts is provided to download and process that database (or others) into a useable format.
To configure these scripts to run on your computer, run the interactive configure script.
Afterwards, run make database to build the database tables for the metaproteomics webserver or make index to build the index files for the metagenomics pipeline. Running just make will create both.
To safe some space, run make clean_intermediates afterwards to remove intermediate files.
The make-on-hpc.sh script contains information on how to run this on our own high performance computing infrastructure.