From 464ec54432432e3d0ac09c81c9ecc6352298461d Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Tue, 3 Oct 2023 12:30:40 +0200 Subject: [PATCH] better instructions for prerequisites --- README.rst | 9 ++++++--- ReadMe.md | 9 ++++++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index 761d0f67..55f5603c 100644 --- a/README.rst +++ b/README.rst @@ -41,11 +41,14 @@ Prerequisites Oktoberfest requires python >=3.8,<=3.11. Best practise is to use a clean conda environment (`Miniconda `_). -If you provide thermo raw files, make sure `ThermoRawFileParser `_ is installed. +If you provide RAW files, you need ThermoRawFileParser for conversion to mzML. +Please download the latest release from the `github repository `_ 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 `_ is installed. +To make ThermoRawFileParser work on linux or MacOS, make sure mono `mono `_ is installed. -If you want to use percolator, make sure you install version 3.06.1 (`percolator `_). +If you want to use percolator for rescoring, make sure you install version 3.06.1 (`percolator `_). Using pip (recommended) ~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/ReadMe.md b/ReadMe.md index bc207f44..5ab2318e 100644 --- a/ReadMe.md +++ b/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)