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Sample configurations for using ABM

Automated Benchmarking, or ABM, is a command-line tool that automates and tracks the benchmarking process for workflows in Galaxy.

In this repository you will find complete examples on how to use ABM.

One-time ABM setup

If you do not have ABM installed already, start by installing and configuring it. You can also find these instructions in the ABM documentation.

  1. Install ABM
python3 -m venv .venv
source .venv/bin/activate
pip install gxabm
  1. Obtain your API keys from the Galaxy servers and add them to the ~/.abm/profile.yml file. Here is a sample profile file for usegalaxy.org and usegalaxy.org.au.
usa:
  url: https://usegalaxy.org
  key: your_Galaxy_US_api_key
australia:
  url: https://usegalaxy.org.au
  key: your_Galaxy_AU_api_key
  1. Clone this repository. Optionally you can copy the Workflow and History configurations to ~/.abm. The two configuration files contain links to the relevant workflows and inputs for the workloads we will benchmark. If you already have ABM installed you will need to edit your ~/.abm/workflows.yml and ~/.abm/histories.yml files to add the workflows and histories you want to use for benchmarking.
git clone https://github.com/SchatzLabJHU/abm-examples.git
cd abm-examples
cp .abm/histories.yml .abm/workflows.yml ~/.abm/  # Optional

Run benchmarks

With the necessary configurations done, let's run a performance comparison experiment. An ABM Experiment defines which benchmarks we want to run, on which Galaxy servers, and how many times. You can find the Experiment definition in the experiments folder. For the vc (Variant Calling) experiment, ABM will import a variant calling workflow to the Galaxy servers defined above, upload some sample data, and invoke the workflow. It will then monitor the workflow as it runs and, once complete, download the runtime data for each tool. The summarize sub-command will consolidate and present the results. The data can also be downloaded in a CSV format for downstream analysis in other tools.

  1. Upload the workflow and history to the Galaxy server
for server in usa australia; do
    abm $server workflow import variant
    abm $server history import variant-2g
done
  1. Run the experiment
abm experiment run experiments/vc.yml

  1. Wait for the run experiment command to finish. This will take a while.

  2. View a summary of the results

abm experiment summarize metrics/experiment name

NOTE: The European and Australian servers do not currently have metrics installed so the summarize command will not generate any results.

Changing experiment configuration

If you would like to change this workflow or input data is used for the benchmarks, simply edit the ~/.abm/workflows.yml and ~/.abm/histories.yml files from above to point to your desired workflow. You will also need to change the contents of benchmarks/vc.yml to update the name of the workflow and its inputs.