Installing the GUANinE Benchmark

tl;dr

GUANinE datasets are built on Git and Git LFS; optional (recommended) packages are twobitreader, scipy, pandas, and transformers – but feel free to use your own tool to parse sequences, tally results, read files, and load models (respectively).

example installation

  1. Most systems (Colab, HPC, etc) come pre-packaged with Git, but you should consult Git’s documentation if which git returns nothing in your console.

  2. Next, to install Git LFS, you should try:

    git lfs install

If this returns an error, it means your system can’t find the proper installation files (rip). Those using conda/mamba can try conda install git-lfs. Alternatively, for mac you can try brew install git-lfs, while for linux check the guide here.

  1. Finally, to install the optional i/o tools with pip:

    pip install twobitreader scipy pandas
pip install transformers