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KeyGenes data processor

A Snakemake based workflow to fetch data from multiple batch-RNA datasets and submit it to a MySQL-database.

Requirements

The pipeline requires programs to installed:

  • MySQL (^8.0)
  • Python (^3.5)
  • R (^3.5)

Installation

The workflow can be cloned from GitHub with the following command

git clone https://github.com/LUMC/KeyGenes-dataprocessor

The python-based requirement can be installed by using:

pip3 install -r requirements.txt

Atlast, the R-based library EdgeR is required; click here for installation instructions.

Instructions

The workflow strictly relies on the settings of a configuration file. All parameters all required. The DB parameters refer to the MySQL user that can be used for interaction with the database. All datasets that are wished to be included in the execution of the pipeline, need to be placed in the input folder. The output folder will contain all the pipeline results.

The config file is typically a yaml (.yml) file and is not restricted to a specific naming.

input:
  - training_adult.txt
  - training_fetal.txt
output_dir: output
DB_HOST: localhost
DB_USERNAME: user
DB_PASSWORD: password

Execution

When everything is configured, the pipeline can be executing using the following command:

snakemake --configfile=<example.yml>

License

MIT