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@jacquayj jacquayj commented Mar 11, 2025

Description of changes:

  • Merge AlphaFold Containers: protein-utils, alphafold-data, and alphafold-predict
  • Update container build scripts
  • Update workflow labels
# Dockerfile info:
# 
# This file is a combination of three Dockerfiles from the original alphafold implementation.
# The first part of the file is from the alphafold-data Dockerfile.
# The second part is from the protein-utils Dockerfile.
# The third part is from the alphafold-predict Dockerfile, with modifications to work on Amazon Linux vs Ubuntu.
# 
# Multiple Python versions are installed in the container to support the different portions of the pipeline
# and their known working pinned dependency versions.

# Python versions installed:
# 3.8.20 - compiled from source, used for label 'protutils' (venv: /opt/venv38-putils)
# 3.9.16 - installed via Miniconda, used for lablel 'predict' (venv: /opt/conda)
# 3.9.20 - installed via yum, used for label 'data' (venv: /opt/venv39-afdata)


# New Python environment locations:
# label 'data':      /opt/venv39-afdata
# label 'protutils': /opt/venv38-putils
# label 'predict':   /app/alphafold${ALPHAFOLD2_VERSION}

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@jacquayj jacquayj marked this pull request as ready for review March 11, 2025 21:57
@jacquayj
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jacquayj commented Mar 11, 2025

The new Dockerfile could be improved:

  • ARG for dep version variable
  • Multiple versions of alphafold installed - one from local build context and the other from git clone. Not sure why the local one is needed
  • Multiple versions of Python - this may be OK, would take a lot of work unify

@jacquayj
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Test runs for af-monomer and af-multimer on HealthOmics finished successfully for this branch

@brianloyal brianloyal merged commit c9e6cbe into aws-samples:main Mar 12, 2025
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2 participants