genben

Benchmarking of systems for storage and compute over large-scale genomic data using the scikit-allel library.

Source Code: https://github.com/ornl-oxford/genben

Setup and Execution

Download genben:

git clone https://github.com/ornl-oxford/genben.git

Install genben:

cd genben

pip install -e .

Run genben:

1. Generate the initial, default configuration file:

   $ genben config --output_config FILEPATH [-f]

   and then edit the newly-created INI file for the benchmarking environment.

2. Setup the benchmark data and the benchmark environment:

   $ genben setup --config_file FILEPATH

3. Run the benchmark:

   $ genben exec --config_file FILEPATH [--label LABEL]}

Benchmark Structure

Benchmark is structured to follow conventions of the authoritative Python benchmark suite.

Benchmark is executed as a command line utility, and configured with an INI configuration file. It contains an FTP downloader module that will attempt to download the benchmark data files from the FTP server, if the module is enabled. If the FTP module is disabled or if the files are already present, the benchmark will read the files from the filesystem. All the results will be recoded as .csv (comma-separated values) for easy loading into analytic suites, or the database.

Data Sources for Benchmarking

VCF files:

• 1000 Genomes Project: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/