alphafold_singularity

Singularity recipe for AlphaFold, with example Slurm job script.

This splits off my pull request google-deepmind/alphafold#166

Disclaimer: this project is not affiliated with DeepMind.

Unfixed bug in Alphafold tagged release 2.2.2

N.B. google-deepmind/alphafold#510 (comment)

Prebuilt Singularity image

A prebuilt image is hosted on cloud.sylabs.io: https://cloud.sylabs.io/library/prehensilecode/alphafold_singularity/alphafold

What This Code Contains

Singularity.def which is the recipe to build the Singularity image. This is a port of the Dockerfile provided by AlphaFold.
run_singularity.py which is a port of the run_docker.py script provided by AlphaFold. It is a wrapper to provide a friendly interface for running the container.

Installation Instructions

Build the Singularity image

Check out this repo into the top of the alphafold source tree to a directory called singularity:

$ cd alphafold-v2.x.x
$ git clone https://github.com/prehensilecode/alphafold_singularity singularity

To use, first install the Python requirements:

$ python3 -m pip install -r singularity/requirements.txt

Then, build the Singularity image:

$ sudo singularity build alphafold.sif singularity/Singularity.def

If your /tmp directory is small, you may need to set the SINGULARITY_TMPDIR environment variable to a directory on a filesystem with more free space. My builds have consumed up to 15 GiB of space. The resulting image file may be up to 10 GiB.

Install and run

To run, modify the $ALPHAFOLD_SRC/singularity/run_singularity.py and change the section marked USER CONFIGURATION. At the least, you will need to modify the values of:

singularity_image - absolute path to the alphafold.sif Singularity image

E.g.

#### USER CONFIGURATION ####
# AlphaFold Singularity image.
singularity_image = Client.load(os.path.join(os.environ['ALPHAFOLD_DIR'], 'alphafold.sif'))

Run as a Slurm job on a cluster

See the example job script example_slurm_job.sh

edoapra/alphafold_singularity