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README.md

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+---
+license: other
+license_name: mixed-upstream-oss
+license_link: https://github.com/ai4nucleome/GLMap
+pretty_name: GLMap scoring containers
+tags:
+- genomics
+- dna
+- genomic-language-model
+- apptainer
+- singularity
+- container
+- bioinformatics
+- reproducibility
+viewer: false
+---
+
+# 🧬 🗺️ GLMap scoring containers
+
+Prebuilt **Apptainer / Singularity** images that carry the GPU runtime
+environments for **scoring all 123 genomic language models (gLMs)** profiled in
+[**GLMap**](https://github.com/ai4nucleome/GLMap) — *Profiling genomic language
+models as individuals in a population*.
+
+The 123 models span runtime stacks that are **mutually incompatible** (Python
+3.8–3.12, PyTorch 1.13–2.9, CUDA 11.7–12.4) and can never share one interpreter.
+These four images package every environment so you can recompute the
+likelihood responses **without setting up a single conda env**.
+
+> Only need the **analysis** (precomputed scores, figures/tables)? You don't
+> need these images at all — `pip install -e .` on the
+> [GLMap repo](https://github.com/ai4nucleome/GLMap) gives a torch-free stack.
+
+## What's here
+
+Each image is **self-contained** (the shared CUDA 12.8 base is already inside;
+download only the group(s) for the models you want to score):
+
+| Image | Size | Envs | Model families |
+|---|---|---|---|
+| `bio-default.sif` | 17 GB | base / dnabert2 / megadna | NT, GENA-LM, ModernBERT, GROVER, Mistral-DNA, NTv3, … (most); DNABERT-2 / DNABERT-S; megaDNA |
+| `bio-cu118.sif`   | 20 GB | caduceus / gf / hyena-dna | Caduceus; GenomeOcean; HyenaDNA |
+| `bio-cu121.sif`   | 15 GB | PlantCAD | PlantCAD2 |
+| `bio-evo.sif`     | 24 GB | evo / evo2 | Evo-1 / Evo-1.5; Evo-2 (7B) |
+
+Each image holds its envs as isolated micromamba environments and dispatches to
+the right one per model via the `GLMAP_ENV` variable.
+
+## Download
+
+```bash
+# one image
+hf download Tim419/GLMap-containers bio-default.sif --repo-type dataset --local-dir .
+
+# or all four
+hf download Tim419/GLMap-containers --repo-type dataset --local-dir .
+```
+
+## Run
+
+Bind your [GLMap checkout](https://github.com/ai4nucleome/GLMap) at `/work`
+(code, panel, audit, model weights) and pick the env with `GLMAP_ENV`:
+
+```bash
+GLMAP_ENV=caduceus apptainer run --nv \
+    --bind "$PWD":/work --pwd /work bio-cu118.sif \
+    scripts/score/scoring_worker.py --from-audit \
+    --hf-ids kuleshov-group/caduceus-ph_seqlen-131k_d_model-256_n_layer-16
+```
+
+Or run the **full 123-model sweep** straight through the images:
+
+```bash
+python scripts/score/run_scoring_sweep.py \
+    --backend container --image-dir <dir with the .sif files> --hf-cache "$HF_HOME"
+```
+
+- `--nv` exposes the host GPU.
+- On compute nodes **without user namespaces**, use `singularity run --nv`
+  (the same `.sif`) — the GLMap sweep takes `--container-runtime singularity`.
+- **HyenaDNA / megaDNA** also need their loader code on the bound checkout: it
+  is in the GLMap repo after `bash models/setup_external_models.sh` (HyenaDNA's
+  is vendored; megaDNA's weight auto-downloads from the HF Hub).
+
+See [`container/README.md`](https://github.com/ai4nucleome/GLMap/blob/main/container/README.md)
+and [`models/env_routing.md`](https://github.com/ai4nucleome/GLMap/blob/main/models/env_routing.md)
+for the full model → image/env routing.
+
+## License
+
+These images bundle many third-party open-source runtimes (PyTorch,
+Transformers, mamba-ssm, flash-attn, evo2, …) and each model family's loader
+code — **each remains under its own upstream license**. The GLMap glue code is
+Apache-2.0. Individual model **weights** are downloaded separately and follow
+their own licenses. Consult each upstream project before redistribution or
+commercial use.
+
+## Citation
+
+```bibtex
+@article{hou2026glmap,
+  title   = {Profiling genomic language models as individuals in a population},
+  author  = {Hou, Yusen and Long, Weicai and Su, Houcheng and Feng, Junning and Zhang, Yanlin},
+  journal = {In submission},
+  year    = {2026}
+}
+```
+
+Project: <https://github.com/ai4nucleome/GLMap> · Panel dataset:
+[`Tim419/GLMap-panels`](https://huggingface.co/datasets/Tim419/GLMap-panels)