adjust README

Author: Felix Van der Jeugt

README.md

@@ -2,11 +2,7 @@
 
 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.
+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.