This module provides the batch scripts of the ColabFold implementation of alphafold.

Documentation

Documentation

Slurm script

Using the package under srun. A batch script can also be used.

$ srun --pty --export ALL -p gpu --gres=gpu:1 bash
$ module load colabfold
$ mkdir -p output
$ colabfold_batch input.fasta output

 

Build instructions for those who are curious

            $ module load python/3.12
            $ module load cuda/12.8
            $ module load gcc
            $ module load openmpi
            $ mkdir -p /mnt/nasapps/production/colabfold/1.5.5
            $ pip3 install --prefix=/mnt/nasapps/production/colabfold/1.5.5 --no-warn-conflicts \
             "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold" \
             "colabfold[alphafold]"
            $ pip3 install --prefix=/mnt/nasapps/production/colabfold/1.5.5 --upgrade \
             "jax[cuda12]"==0.4.35 tensorflow
            $ pip3 install --prefix=/mnt/nasapps/production/colabfold/1.5.5 silence_tensorflow
            $ sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" \
             /mnt/nasapps/production/colabfold/1.5.5/lib/python3.12/site-packages/colabfold/plot.py
            $ sed -i -e "s#appdirs.user_cache_dir(__package__ or \"colabfold\")#Path.home().joinpath(\"colabfold\")#g" \
             /mnt/nasapps/production/colabfold/1.5.5/lib/python3.12/site-packages/colabfold/download.py
            $ sed -i -e "s#from io import StringIO#from io import StringIO\nfrom silence_tensorflow import silence_tensorflow\nsilence_tensorflow()#g" \
             /mnt/nasapps/production/colabfold/1.5.5/lib/python3.12/site-packages/colabfold/batch.py