Measure & compare the performance of sequence alignment workflows

Jan P. Hummel

Technical University of Munich | Technische Universität München

Contact via: jan.hummel@tum.de

Getting started

Follow these steps to set up and configure the environment for your specific needs:

1. Prerequisites

• Install Ruby 3.2.2
• Install bundler gem install bundler
• Install dependencies bundle install
• At least one command line based sequence alignment algorithm

2. Add Configurations

• Create directories mkdir var/config var/results
• Either import benchmarking sequences and pairwise alignments or
• Create benchmarking sequences and pairwise alignments touch var/config/run.yml
• Configure alignment algorithms touch var/config/alignments.yml
• At least one command line based sequence alignment implementation

   # EXAMPLE CONFIGURATION
   commands:
      - java: "PATH_TO_JAVA_EXECUTABLE" # if any implementation requires a specific Java version
      - iterations: NUMBER_OF_ITERATIONS # number of iterations to run the benchmark
      # Define alignment implementations to benchmark:
      - path: "PATH_TO_EXECUTABLE"
        args:
        --[arg_1]: "VALUE_FOR_ARG_1" # arguments to pass to the executable
        #...

3. Run

• Generate samples: ruby .\generate.rb
• Run benchmark test ruby .\main.rb [if jar is used: jar] [path to configuration yaml file]
• Results are written to var/results

© Jan P. Hummel

Jan P. Hummel  ·  GitHub @github4touchdouble  ·  contact via jan.hummel@tum.de