https://github.com/marcelm/dnaio-benchmarks

Benchmarks for every commit of dnaio
https://github.com/marcelm/dnaio-benchmarks

Last synced: 25 days ago
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Benchmarks for every commit of dnaio

• Host: GitHub
• URL: https://github.com/marcelm/dnaio-benchmarks
• Owner: marcelm
• Created: 2022-02-18T22:43:49.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2022-12-13T14:06:05.000Z (over 2 years ago)
• Last Synced: 2025-02-02T18:26:39.519Z (3 months ago)
• Language: Python
• Homepage: https://marcelm.github.io/dnaio-asv/
• Size: 820 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# Benchmark results

[Benchmarks](https://marcelm.github.io/dnaio-benchmarks/) for [dnaio](https://github.com/marcelm/dnaio)

# Download benchmarking datasets

    conda create -n sratools sra-tools

    cd data

    ./download.sh

# Airspeed Velocity (asv)

Some benchmarks are run using [airspeed velocity](http://github.com/airspeed-velocity/asv/).

They are currently run manually on a rented virtual machine somewhere on the internet,

so the measurements are not as reliable as they would be on a dedicated machine.

    python3 -m venv .venv

    source .venv/bin/activate

    pip install asv

To run this, the benchmarking datasets need to be downloaded first. Ensure you have `fastq-dump` available, then run `cd data && ./download.sh` to do so.

Run benchmarks with:

    asv run -k

Publish:

    asv gh-pages

# Running library comparisons

Ensure benchmark data was downloaded as described above.

    conda create -n dnaio-benchmarks python sra-tools

    conda activate dnaio-benchmarks

    grep '^# pip install' comparelibs.py | cut -c15- | xargs pip install  # This is the worst way to do it

    python ./comparelibs.py