Build funannotate2 Docker image (pixi + GitHub Actions)#51
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nextgenusfs merged 6 commits intomainfrom Apr 21, 2026
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April 20, 2026 08:22
Agent-Id: agent-001dbe11-1134-451f-9706-c99fb75eb238
- Dockerfile (linux/amd64, 3 stages: pixi build -> dbs install -> minimal final) - pixi.lock (linux-64, generated in prefix-dev/pixi container) - .github/workflows/docker.yml (workflow_dispatch + v* tag; GHCR + Docker Hub with secret guard) Agent-Id: agent-001dbe11-1134-451f-9706-c99fb75eb238
- Multi-stage Dockerfile (build -> dbs -> final) targeting linux/amd64 - pixi.lock generated in ghcr.io/prefix-dev/pixi container (linux-64 only) Agent-Id: agent-001dbe11-1134-451f-9706-c99fb75eb238
Agent-Id: agent-001dbe11-1134-451f-9706-c99fb75eb238
Adds a pull_request trigger to docker.yml scoped to Dockerfile, pixi config, and the workflow file itself, so image builds are validated on PRs touching container-relevant files without running on every commit. PRs build-only (no registry push); pushes happen only on tag push or workflow_dispatch.
- README: promote Docker to primary install path; add pixi install recipe; relabel the bioconda section as Linux (conda). - docs/installation.rst: new 'Using the Docker image' and 'Installing with pixi' sections at the top; keep existing conda and pip instructions intact. Agent-Id: agent-001dbe11-1134-451f-9706-c99fb75eb238
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Summary
Adds a fully-functional
nextgenusfs/funannotate2Docker image assembled with pixi, plus a GitHub Actions workflow that builds and publishes it to GHCR (and Docker Hub onceDOCKERHUB_USERNAME/DOCKERHUB_TOKENsecrets are set).See the spec for full design rationale and verification notes.
Files added
pixi.toml/pixi.lock— pixi workspace with bioconda tooling (augustus, minimap2, miniprot, snap, glimmerhmm, diamond, trnascan-se, table2asn, pytantan, …), python deps (gfftk, gapmm2, buscolite, pyhmmer, pyfastx, tensorflow 2.10–2.15), and PyPI packages (funannotate2source,funannotate2-addons,helixerlite,annorefine).Dockerfile— three-stage build:pytantanfrom source with-DHAVE_AVX2:BOOL=OFFso it runs on any x86_64 host (incl. Rosetta 2 on Apple Silicon).funannotate2 install -d allinto/opt/funannotate2_dbon a dedicated layer (~3 GB; BUSCO lineages download at runtime).ubuntu:22.04with the pixi env, databases, and captured activation script via tini..dockerignore— keeps the build context slim..github/workflows/docker.yml— builds on tag pushv*,workflow_dispatch, and paths-filtered PRs (Dockerfile / pixi.* / docker.yml). PRs build-only; tag and dispatch push to GHCR (+ Docker Hub if secret is present).Notable design choices
linux/amd64only — bioconda coverage on arm is incomplete; target is HPC Linux x86_64. Apple Silicon users run under Rosetta.predict/annotatefetch on demand; docs will describe mounting a host cache dir.Local verification (Docker Desktop on Apple Silicon, Rosetta 2)
docker build --target buildsucceeds (~3 min; pixi resolves lockfile, pytantan SSE4 rebuild ~23 s)funannotate2 --help,funannotate2 install -s,f2a --help,helixerlite --helpall exit 0pytantan+RepeatFinder(default_scoring_matrix())instantiates cleanlydbsstage withfunannotate2 install -d all) will be validated by this PR's CI run on native x86_64.Follow-ups (after this merges and the image is verified)
DOCKERHUB_USERNAME+DOCKERHUB_TOKENrepo secrets to enable Docker Hub publishing.docs/installation.rstandREADME.mdwith pixi and Docker install instructions.althonos/pytantanabout the AVX2-only wheels (draft ready in workspace notes).Pull Request opened by Augment Code with guidance from the PR author