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AlphaFold Singularity Container

This repo provides definition files to build a singularity container of AlphaFold v2 (https://github.com/deepmind/alphafold) that will run and be easy to invoke in the NMRbox environment.

Build instructions from non-docker setting by kalininalab were used.

Build container

# build base container
sudo /usr/software/singularity/bin/singularity build base.sif base.def
# build alphafold container
sudo /usr/software/singularity/bin/singularity build alphafold.sif alphafold.def

Run AlphaFold

./alphafold.py /path/to/fasta/file

Notes

  • The alphafold.py run script has no requirements and should run in vanilla python 3.8.
  • The run script allows customizing the database location and max_template_date. Call with -h to see usage information.
  • By default, this uses the monomer model for monomers and the multimer model for multimers, and uses the full_dbs option for better quality results. For more details, see https://github.com/deepmind/alphafold#running-alphafold