diff --git a/Dockerfile b/Dockerfile index d0bc498..44b5e01 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,10 @@ # Target: linux/amd64 (x86_64 Linux / HPC) ARG PIXI_VERSION=0.67.0 -ARG UBUNTU_VERSION=22.04 +# Ubuntu 24.04 (noble) is required for augustus 3.5.0 from apt +# (22.04/jammy only has 3.4.0). augustus is intentionally installed via apt +# rather than bioconda — see pixi.toml and the final stage below for details. +ARG UBUNTU_VERSION=24.04 # --------------------------------------------------------------------------- # Stage 1: build — resolve + install the pixi environment from pixi.lock @@ -108,12 +111,19 @@ ENV DEBIAN_FRONTEND=noninteractive \ LANG=C.UTF-8 \ LC_ALL=C.UTF-8 +# augustus + augustus-data are installed from Ubuntu apt rather than bioconda. +# The bioconda augustus 3.5.0 binary is built with a modern x86_64 microarch +# baseline (AVX2/BMI2) and SIGILLs under Rosetta 2 on Apple Silicon and on +# pre-Haswell x86_64. Ubuntu noble's augustus 3.5.0+dfsg targets a generic +# x86_64 baseline and runs on every host where this image lands. RUN apt-get update && \ apt-get install -y --no-install-recommends \ ca-certificates \ tini \ procps \ - wget && \ + wget \ + augustus \ + augustus-data && \ rm -rf /var/lib/apt/lists/* # Pixi env (python + bioconda tooling + funannotate2 + addons + helixerlite) @@ -123,8 +133,12 @@ COPY --from=build /app/bin/entrypoint.sh /app/bin/entrypoint.sh # Pre-built databases (~3 GB; BUSCO lineages download at runtime) COPY --from=dbs /opt/funannotate2_db /opt/funannotate2_db +# AUGUSTUS_CONFIG_PATH points at the apt-shipped config tree. funannotate2's +# config.py derives AUGUSTUS_BASE from dirname(AUGUSTUS_CONFIG_PATH)+"/scripts", +# which resolves to /usr/share/augustus/scripts where the apt augustus package +# installs new_species.pl, optimize_augustus.pl, etc. ENV FUNANNOTATE2_DB=/opt/funannotate2_db \ - AUGUSTUS_CONFIG_PATH=/app/.pixi/envs/default/config \ + AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config \ PATH=/app/.pixi/envs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin WORKDIR /data diff --git a/funannotate2/train.py b/funannotate2/train.py index 2de5307..21ceaa7 100755 --- a/funannotate2/train.py +++ b/funannotate2/train.py @@ -433,7 +433,6 @@ def buscolite( cpus=cpus, offset=flanks, logger=log, - check_augustus=False, verbosity=1, ) log.info( diff --git a/pixi.lock b/pixi.lock index 6b4b642..804084f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -17,7 +17,6 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_3.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda - - conda: https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321h9716f88_9.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-ha62d5e7_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda @@ -28,18 +27,13 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.10-h8b1a151_0.conda - 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The bioconda +# augustus binary targets a modern x86_64 microarch (AVX2/BMI2) and SIGILLs +# under Rosetta 2 on Apple Silicon and on pre-Haswell CPUs. The Docker image +# installs augustus from Ubuntu apt instead (generic-baseline build, runs +# everywhere). On native macOS development the funannotate2 CLI is exercised +# via the dockerized image, so augustus on osx-arm64 is not needed here. minimap2 = "*" miniprot = "*" snap = "*" @@ -20,8 +25,10 @@ diamond = "*" trnascan-se = "*" # funannotate2 python deps available via bioconda / conda-forge +# NOTE: buscolite is installed via pypi (see [pypi-dependencies]) because its +# bioconda recipe pulls in augustus as a hard dependency, which we deliberately +# avoid (see comment above). The pypi package has no such dep. gapmm2 = ">=26.5.22" -buscolite = ">=26.4.22" pyhmmer = ">=0.12.0" pyfastx = ">=2.0.0" gb-io = ">=0.3.2" @@ -52,6 +59,8 @@ funannotate2 = { path = ".", editable = false } "funannotate2-addons" = "*" helixerlite = "*" annorefine = ">=2026.2.9" +# buscolite via pypi to avoid its bioconda recipe's augustus dependency +buscolite = ">=26.4.22" # pytantan: built from the nextgenusfs/pytantan fork, which adds a # `PYTANTAN_DISABLE_SIMD` CMake option and a `PYTANTAN_SIMD` env-var override. # The PyPI wheels ship with AVX2 enabled and SIGILL under Rosetta 2 on Apple