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Bioinformatics Benchmark Suite

A suite for testing bioinformatics tools. Be sure to check a suite's individual README for any additional requirements. Their README's are stored in their individual folders located here.

Requirements

  • python 3.8 or higher
  • pip

Furthermore, ensure that the python /bin folder is added to $PATH in .bash_profile so that the tool will be executable from the command line.

How-to

Install

git clone git@github.com:molgenis/biobesu.git
cd biobesu
pip install .

Use

# General format
biobesu <suite> <runner> --<runner_argument> [--<runner_optional_argument>]

# Get available suites
biobesu

# Get runners for selected suite
biobesu <suite>

There are several scripts which can be executed directly. Do note that some of these require entry_points from the setup.py to function correctly, so installing BioBeSu with pip is still required.

Example:

# Prepare lirical.
java -jar LIRICAL.jar download

# Run lirical with benchmark data.
biobesu hpo_generank lirical --jar /path/to/lirical-1.3.0/LIRICAL.jar \
--hpo /path/to/hp.obo --input /path/to/benchmark_data.tsv \
--output /path/to/dir/output --lirical_data /path/to/dir/lirical/data \
--runner_data /path/to/tmp/dir/

Developers (work-in-progress)

Installation

Command line

git clone git@github.com:molgenis/biobesu.git
cd biobesu
python3 -m venv venv
source venv/bin/activate
pip install --editable '.[test]'

Testing

Command line

source venv/bin/activate  # if not yet loaded
pytest test/

IDEs

When running the tests through an IDE, be sure pytest is selected!

In PyCharm/IntelliJ IDEA: Preferences -> Tools -> Python Integrated Tools -> Default test runner

Structure

helper/ # General helper scripts
    |- <name>.py

suite/ # Benchmark suites
    |- <suitename>
        |- cli.py # Entry point for suite
        |- helper/ # Suite helper scripts
            |- <name>.py
        |- runner/ # Scripts runnable through suite entry point
            |- <name>.py

When updating the setup.py with a new suite, be sure to use the naming convention: biobesu_<dirname_suite>. You can deviate within a suite in regards to the entrypoint names, though it is suggested to keep them identical (or at least similar).

setup.py example

'biobesu_suites': [
    'suit_name = biobesu.suite.suit_name.cli:main',
],
'biobesu_suit_name': [
    'runner_name = biobesu.suite.suit_name.runner.runner_name:main',
    'another = biobesu.suite.suit_name.runner.another_runner:main'
],

For test python scripts, please prepend <suit_name>- before the name if it's a suite-specific test file. This so that no overlapping test script filenames can occur.