Dockerfile

FROM julia:1.10.9-bullseye AS base

ARG BRANCH=main

ENV JULIA_PROJECT=/app \
    JULIA_DEPOT_PATH=/usr/local/share/julia

RUN apt-get update \
 && apt-get install --no-install-recommends -y git \
 && rm -rf /var/lib/apt/lists/* \
 && git clone --depth 1 --no-tags --single-branch -b $BRANCH https://gitlab.pasteur.fr/nyx/larvatagger.jl "$JULIA_PROJECT" \
 && rm -rf "$JULIA_PROJECT/.git" \
 && julia -e 'using Pkg; try Pkg.rm("TaggingBackends"); catch end; Pkg.instantiate()' \
 && ln -s "$JULIA_PROJECT/scripts/larvatagger" /bin \
 && mkdir -p "$JULIA_DEPOT_PATH/logs" && rm -f "$JULIA_DEPOT_PATH/logs/manifest_usage.toml" && ln -s /dev/null "$JULIA_DEPOT_PATH/logs/manifest_usage.toml"

# RUN $JULIA_PROJECT/test/precompile.sh --shallow \
#  && mv larvatagger.so /lib/ \
#  && rm -rf $JULIA_PROJECT/test/data

ENTRYPOINT ["/app/scripts/larvatagger"]
#, "-J/lib/larvatagger.so"]


FROM base AS prebuild

ENV PIP_DISABLE_PIP_VERSION_CHECK=1 \
    PIP_NO_CACHE_DIR=1 \
    POETRY_VIRTUALENVS_IN_PROJECT=1 \
    POETRY_VERSION=1.8.3

RUN apt-get update \
 && apt-get install --no-install-recommends -y python3-dev python3-pip \
 && rm -rf /var/lib/apt/lists/* \
 && pip install "poetry==$POETRY_VERSION"


FROM prebuild AS backend

ARG PROJECT_DIR=/app
ARG TAGGINGBACKENDS_BRANCH=main
ARG BACKEND

RUN if [ -z $TAGGINGBACKENDS_BRANCH ]; then \
    TAGGINGBACKENDS_BRANCH=dev; \
    fi; \
    if [ "$BACKEND" = "MaggotUBA/20221005-1" ]; then \
    cd /app \
 && julia -e "using Pkg; Pkg.add(url=\"https://gitlab.pasteur.fr/nyx/TaggingBackends\", rev=\"$TAGGINGBACKENDS_BRANCH\")" \
 && git clone --depth 1 --no-tags --single-branch -b 20221005 https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
 && cd MaggotUBA \
 && rm -rf .git \
 && rm -rf models/20221005 \
 && poetry install --only main \
 && poetry add "pynvml==11.4.1" \
 && rm -rf ~/.cache; \
    elif [ "$BACKEND" = "MaggotUBA/20221228" ]; then \
    cd /app \
 && julia -e "using Pkg; Pkg.add(url=\"https://gitlab.pasteur.fr/nyx/TaggingBackends\", rev=\"$TAGGINGBACKENDS_BRANCH\")" \
 && git clone --depth 1 --no-tags --single-branch -b dev https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
 && cd MaggotUBA \
 && rm -rf .git \
 && poetry install --only main \
 && poetry add "pynvml==11.4.1" \
 && apt-get update \
 && apt-get install --no-install-recommends -y wget \
 && mkdir -p models \
 && cd models \
 && wget -O- https://gitlab.pasteur.fr/nyx/artefacts/-/raw/master/MaggotUBA/20221228.tar.gz?inline=false | tar zxv \
 && apt-get autoremove -y wget \
 && rm -rf /var/lib/apt/lists/* \
 && rm -rf ~/.cache; \
    elif [ "$(echo $BACKEND | cut -d/ -f1)" = "MaggotUBA" ]; then \
    cd /app \
 && julia -e "using Pkg; Pkg.add(url=\"https://gitlab.pasteur.fr/nyx/TaggingBackends\", rev=\"$TAGGINGBACKENDS_BRANCH\")" \
 && git clone --depth 1 --no-tags --single-branch -b $(echo $BACKEND | cut -d/ -f2) https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
 && cd MaggotUBA \
 && rm -rf .git \
 && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') \
 && poetry install --only main \
 && poetry add "pynvml==11.4.1" \
 && if [ "$(echo $BACKEND | cut -d/ -f2)" = "main" ] || [ "$(echo $BACKEND | cut -d/ -f2)" = "dev" ]; then \
    julia -e 'using Pkg; Pkg.add("JSON3")' \
 && scripts/make_models.jl default \
 && cd /app \
 && recipes/patch.sh; \
    fi \
 && rm -rf ~/.cache; \
    fi

COPY recipes/checkgpu /bin/


FROM backend AS confusion

ARG PYTHON_ENV=/app/MaggotUBA

RUN test -d $PYTHON_ENV \
 && cd $PYTHON_ENV \
 && poetry add "scikit-learn==1.3.0" \
 && rm -rf ~/.cache

ADD https://gitlab.pasteur.fr/nyx/TaggingBackends/-/raw/dev/scripts/confusion.py?ref_type=heads&inline=false /bin/confusion.py