git clone https://github.com/CatMOD/CatMOD.git
cd CatMOD
conda create -n catmod -y python=3.9
python setup.py install

git clone https://github.com/CatMOD/CatMOD.git
cd CatMOD
conda env create -f catmod.yml

git clone https://github.com/CatMOD/CatMOD.git
conda create -n catmod -y python=3.9 catboost h5py numpy pysam rich scipy
conda activate catmod

guppy_basecaller --input_path $fast5_folder --recursive --fast5_out --save_path $guppy_folder --flowcell $FLOWCELL --kit $KIT --num_callers $THREADS
multi_to_single_fast5 --input_path $guppy_folder --save_path $single_folder --threads $THREADS --recursive
tombo resquiggle --rna --processes $threads --overwrite --fit-global-scale --include-event-stdev $single_folder $REFERENCE

catmod data_process

catmod extract_features --bed $sample_bed --ref $REFERENCE --align $ont_bam --current $ont_current --threads $THREADS --output $datasets_folder

catmod predict --bed $sample_bed --datasets $datasets_folder --model /path/to/CatMOD/models/wheat_pretrained.cbc.cbm --threads $THREADS --output $datasets_folder