git clone git@github.com:gersteinlab/dna.git
cd dna
mkdir data
cd data
wget https://bydna.s3.us-east-2.amazonaws.com/bert_hg38.tar.gz
tar -xzvf bert_hg38.tar.gz
wget https://bydna.s3.us-east-2.amazonaws.com/dnabert2_bin.tar.gz
tar -xzvf dnabert2_bin.tar.gz

Change the dataset.text_file for configs/experiment/xxx/xxx.yaml

RUN

pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 
pip install -r requirements.txt --no-deps
pip install pytorch-lightning==1.8.6 --no-deps
pip install packaging --no-deps
pip install flash_attn --no-build-isolation --no-deps
pip install lightning_utilities --no-deps
pip install torchmetrics
pip install tensorboardX

small dataset:

python3 train.py experiment='dnabert2/dnabert2_hg38_pretrain' wandb=null trainer.devices=8 > output_small.txt

or

medium dataset:

python3 train.py experiment='dnabert2/dnabert2_pretrain' wandb=null trainer.devices=8