SILOSim utilizes Snakemake pipelines complemented by Python scripts for input validation, configuration file generation, and execution of the workflow.
Coming soon.
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Clone the GitHub repository:
git clone https://github.com/microbialARC/SILOSim cd SILOSim -
Install SILOSim using the installation script:
bash install.sh
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Activate SILOSim environment and display help message:
conda activate silosim silosim -h
When you clone the GitHub repository, you receive SILOSim's core scripts and configuration files (YAML files) that specify which bioinformatics tools are needed for each function. The installation script then creates a conda environment named silosim and installs SILOSim along with Snakemake and its dependencies in silosim conda environment.
The bioinformatics tools themselves are not installed during this installation. When you first run a function (e.g., Strain Identifier or Genome Profiler), Snakemake will automatically download and install only the tools required for that specific function. This minimizes disk space usage, but requires internet connection when running the function.
Think of it like having a recipe book at home. You only buy the specific ingredients when you decide to cook a particular dish, rather than stocking your pantry with every ingredient for every recipe.