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Update README.md
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@vasicek58
vasicek58 authored Dec 9, 2024
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Expand Up @@ -10,7 +10,7 @@ The pipeline requires Snakemake and Conda installed. You can install these follo

1. Format your PSMs or peptides in a tab-separated file as described below
2. Clone the PeptideAnnotator repository: `git clone https://github.com/ProGenNo/ProHap_PeptideAnnotator.git; cd ProHap_PeptideAnnotator`
3. Create a new configuration file based on the instructions in _config_example.yaml_
3. Create a new configuration file called `config.yaml` placed in the root of this repository (next to _Snakefile_) using [https://progenno.github.io/ProHap_PeptideAnnotator/](https://progenno.github.io/ProHap_PeptideAnnotator/), or based on the instructions in _config_example.yaml_
4. Provide the path to the configuration file on line 2 of _Snakefile_
5. Activate the Conda environment to run Snakemake: `conda activate snakemake`
6. Test Snakemake with a dry-run: `snakemake -c1 -n -q`
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