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Scanneo2 is a snakemake workflow for detecting neoantigens from multiple sources. These include
Scanneo2 requires snakemake and snakedeploy which are most easily installed using the Mamba Package Manager (or by conda itself). If neither mamba nor conda is present, it is best to install it from Mambaforge. We provide an environment.yml which allows creating a mamba directory that includes the above-defined dependencies.
Simply, run
mamba env create --file https://raw.githubusercontent.com/ylab-hi/ScanNeo2/main/environment.yml
mamba activate scanneo2
In the following Scanneo2 needs to be deployed. For that, create a working directory and enter it, e.g.
mkdir -p /path/to/working/directory/
cd /path/to/working/directory/
Now the workflow needs to be deployed which can be done using
snakedeploy deploy-workflow https://github.com/ylab-hi/scanneo2 . --tag v0.1.0
Snakedeploy will create two folders workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs. Later, when executing the workflow, Snakemake will automatically find the main Snakefile in the workflow subfolder.
To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file. It is to be noted that each parameter can also be specified over the command line. For a detailed description of the parameters, please refer to section about the configuration in the wiki. Different locations of configuration files can be specified using --configfile config.yaml. In addition, the paramters can also be specified using the command line such as --config parameter=value.
Given that the workflow has been properly deployed and configured, it can be executed as follows.
For running the workflow while deploying any necessary software via conda (using the Mamba package manager by default), run Snakemake with
snakemake --cores all --use-conda
Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment