evo2

Workspace-local gateway for the Evo 2 repository at /home/vimalinx/Projects/bio_studio/repositories/active/evo2. The repo includes the upstream README, examples/run_evo2.py, and a phage_gen/ subproject, but the current Python environment is not fully ready for direct imports.

Quick Start

• Repository: /home/vimalinx/Projects/bio_studio/repositories/active/evo2
• Documented repo check: python -m evo2.test.test_evo2_generation --model_name evo2_7b
• Docker path: docker build -t evo2 .

When To Use This Tool

• Scoring DNA sequences with Evo 2 forward passes
• Extracting embeddings for downstream genomics tasks
• Generating new DNA sequence continuations from prompts
• Exploring the local Evo 2 phage-design subproject

Common Patterns

# Build the local Evo 2 Docker image from the repo
cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2
docker build -t evo2 .

# Run the upstream generation smoke test after installation
python -m evo2.test.test_evo2_generation --model_name evo2_7b

# Run the local example script inside a prepared Evo 2 environment/container
python /home/vimalinx/Projects/bio_studio/repositories/active/evo2/examples/run_evo2.py

Recommended Workflow

1. Decide first whether you want a native install or Docker-based execution.
2. Satisfy the upstream prerequisites before trying imports: CUDA-capable Linux plus the extra inference dependencies the README calls out.
3. Verify the installation with the upstream test module before running custom examples.
4. Use examples/run_evo2.py for workspace-local scoring, generation, and embedding patterns, and use phage_gen/ only after the base Evo 2 stack is working.

Guardrails

• Direct local import currently fails: import evo2 raised ModuleNotFoundError: No module named 'vortex'.
• Docker images are not prebuilt in this workspace. docker image inspect evo2 failed with No such image: evo2:latest.
• The upstream README requires Linux, CUDA 12.1+, Python 3.12, and additional packages such as Transformer Engine and Flash Attention.
• The 40b checkpoints require multiple GPUs. The example script recommends smaller checkpoints like evo2_1b_base for limited VRAM.
• The local phage_gen/ project depends on Evo 2 being operational first; it is not a self-contained replacement for the base repo setup.