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codonfm-setup

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Set up the public CodonFM v1 repository and download public Encodon checkpoints. Use for requests to build or launch the CodonFM development container, configure local data/checkpoint mounts, verify GPU access, or download public Encodon 80M, 600M, 1B, or Cdwt-1B weights. Do not use for Decodon, Encodon 5B/10B, missense-aggregation, or codon-optimization setup because those implementations are not in the public repository.

skills/bionemo-codonfm-setup/SKILL.md

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Repository last updated
Nov 6, 2026
License
Apache-2.0

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# CodonFM public setup

Operate from the public CodonFM repository root. Support only the checked-in
public v1 code and public Encodon checkpoints.

## Instructions

1. Determine whether the user wants instructions, a downloaded checkpoint, a
   working model environment, or a combination of these.
2. For setup instructions or runtime work, inspect the supplied files and
   configuration directly: the [runner](../../src/runner.py),
   [model configuration](../../src/config.py), [Dockerfile](../../Dockerfile),
   [launcher](../../run_dev.sh), and [requirements](../../requirements.txt).
   Runtime setup requires a checkout; a supplied source archive is sufficient
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