better instructions for prerequisites

README.rst

@@ -41,11 +41,14 @@ Prerequisites
 
 Oktoberfest requires python >=3.8,<=3.11. Best practise is to use a clean conda environment (`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
 
-If you provide thermo raw files, make sure `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ is installed.
+If you provide RAW files, you need ThermoRawFileParser for conversion to mzML.
+Please download the latest release from the `github repository <https://github.com/compomics/ThermoRawFileParser>`_ using the provided zip file and unpack it in the desired location.
+On linux and MacOS, the default location is "/opt/compomics/". On Windows, the default location is the directory from which Oktoberfest is executed.
+You can provide the location of the executable in the config file when starting an Oktoberfest run.
 
-If you are on linux or MacOS, make sure `mono <https://www.mono-project.com/>`_ is installed.
+To make ThermoRawFileParser work on linux or MacOS, make sure mono `mono <https://www.mono-project.com/>`_ is installed.
 
-If you want to use percolator, make sure you install version 3.06.1 (`percolator <https://github.com/percolator/percolator/releases/tag/rel-3-06-01>`_).
+If you want to use percolator for rescoring, make sure you install version 3.06.1 (`percolator <https://github.com/percolator/percolator/releases/tag/rel-3-06-01>`_).
 
 Using pip (recommended)
 ~~~~~~~~~~~~~~~~~~~~~~~

ReadMe.md

@@ -16,11 +16,14 @@
 
 Oktoberfest requires python >=3.8,<=3.11. Best practise is to use a clean conda environment (https://docs.conda.io/en/latest/miniconda.html).
 
-If you provide thermo raw files, make sure ThermoRawFileParser(https://github.com/compomics/ThermoRawFileParser) is installed.
+If you provide RAW files, you need ThermoRawFileParser for conversion to mzML.
+Please download the latest release from the github repository (https://github.com/compomics/ThermoRawFileParser) using the provided zip file and unpack it in the desired location.
+On linux and MacOS, the default location is "/opt/compomics/". On Windows, the default location is the directory from which Oktoberfest is executed.
+You can provide the location of the executable in the config file when starting an Oktoberfest run.
 
-If you are on linux or MacOS, make sure mono (https://www.mono-project.com/) is installed.
+To make ThermoRawFileParser work on linux or MacOS, make sure mono (https://www.mono-project.com/) is installed.
 
-If you want to use percolator, make sure you install version 3.05 (https://github.com/percolator/percolator/releases/tag/rel-3-05)
+If you want to use percolator for rescoring, make sure you install version 3.06.1 (https://github.com/percolator/percolator/releases/tag/rel-3-06-01).
 
 ### Using pip (recommended)