/alphafold_singularity

Primary LanguagePython

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.

Setup

Clone repository into your home directory and cd into the cloned folder.

Build container

export APPTAINER_CACHEDIR=$PWD
export TMPDIR=$PWD
# build base container
apptainer build base.sif base.def
# build alphafold container
apptainer build alphafold.sif alphafold.def

Run AlphaFold Job

Customize or add the following options to a typical CHTC HTCondor submit file:

universe = container
container_image = alphafold.sif
requirements = (HasGpulabData == true)

transfer_executable = false
# replace with multimer.sh if applicable
executable = /opt/alphafold/monomer.sh
arguments = /gpulab_data/alphafold FASTA_file 

transfer_input_files = alphafold.sif, FASTA_file

# request CPUs, GPUS, etc.

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