Metadata-Version: 2.1
Name: Benchmark-4dn
Version: 0.5.15
Summary: Benchmark functions that returns total space, mem, cpu given                 input size and parameters for the CWL workflows
Home-page: https://github.com/SooLee/Benchmark/
Author: Soo Lee
Author-email: duplexa@gmail.com
License: MIT
Description: The repo contains a benchmarking script for some of the CWL workflows used by 4DN-DCIC (https://github.com/4dn-dcic/pipelines-cwl), that returns total space, mem and CPUs required per given input size and a recommended AWS EC2 instance type.
        
        [![Build Status](https://travis-ci.org/SooLee/Benchmark.svg?branch=master)](https://travis-ci.org/SooLee/Benchmark)
        
        ### Example usage of benchmarking script
        * importing the module
        ```python
        from Benchmark import run as B
        ```
        
        * md5
        ```python
        app_name = 'md5'
        input_json = {'input_size_in_bytes': {'input_file': 20000}}
        B.benchmark(app_name, input_json)
        ```
        ```
        {'aws': {'recommended_instance_type': 't2.xlarge', 'EBS_optimized': False, 'cost_in_usd': 0.188, 'EBS_optimization_surcharge': None, 'mem_in_gb': 16.0, 'cpu': 4}, 'total_size_in_GB': 14.855186462402344, 'total_mem_in_MB': 13142.84375, 'min_CPU': 4}
        ```
        
        * fastqc-0-11-4-1
        ```python
        app_name = 'fastqc-0-11-4-1'
        input_json = {'input_size_in_bytes': {'input_fastq':20000},
                      'parameters': {'threads': 2}}
        B.benchmark(app_name, input_json)
        ```
        ```
        {'recommended_instance_type': 't2.nano', 'EBS_optimized': False, 'cost_in_usd': 0.006, 'EBS_optimization_surcharge': None, 'mem_in_gb': 0.5, 'cpu': 1}
        ```
        
        * bwa-mem
        ```python
        app_name = 'bwa-mem'
        input_json = {'input_size_in_bytes': {'fastq1':93520000,
                                              'fastq2':97604000,
                                              'bwa_index':3364568000},
                      'parameters': {'nThreads': 4}}
        B.benchmark(app_name, input_json)
        ```
        ```
        {'aws': {'cost_in_usd': 0.188, 'EBS_optimization_surcharge': None, 'EBS_optimized': False, 'cpu': 4, 'mem_in_gb': 16.0, 'recommended_instance_type': 't2.xlarge'}, 'total_mem_in_MB': 12834.808349609375, 'total_size_in_GB': 15.502477258443832, 'min_CPU': 4}
        ```
        
        To use Benchmark in from other places, install it as below.
        ```
        pip install Benchmark-4dn
        ```
        or
        ```
        pip install git+git://github.com/SooLee/Benchmark.git
        ```
        
        
        ---
        
        Note: From `0.5.3` we have a new function that takes in cpu and memory and returns a sorted list of instance dictionaries.
        ```
        get_instance_types(cpu=1, mem_in_gb=0.5, instances=instance_list(), top=10, rank='cost_in_usd')
        ```
        
        Keys in each instance dictionary:
        ```
        'cost_in_usd', 'mem_in_gb', 'cpu', 'instance_type', 'EBS_optimized', 'EBS_optimization_surcharge'
        ```
        
Keywords: benchmark,cwl,common workflow language,docker,tibanna,bioinformatics,4dn
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
