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.
Run ./run.sh database to build the database tables for the metaproteomics webserver or ./run.sh index to build the index files for the metagenomics pipeline. The top of the run.sh script lists some parameters you might want to change, such as the target location of the files.
The make-on-hpc.sh script contains information on how to run this on our own high performance computing infrastructure.