V.1.1.1

.dockerignore

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+.git
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+build/
+dist/
+*.egg-info/
+output/
+*.sif
+*.sqsh

.gitignore

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+__pycache__/
+*.py[cod]
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+
+output/
+workflow/results/
+workflow/.snakemake/
+
+*.sif
+mono_crash.*.json

Dockerfile

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+FROM python:3.11-slim-bullseye
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONPATH=/opt/metaxtract
+ENV PATH=/opt/venv/bin:$PATH
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        ca-certificates \
+        dirmngr \
+        gnupg \
+    && gpg --homedir /tmp --no-default-keyring \
+        --keyring gnupg-ring:/usr/share/keyrings/mono-official-archive-keyring.gpg \
+        --keyserver hkp://keyserver.ubuntu.com:80 \
+        --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF \
+    && chmod +r /usr/share/keyrings/mono-official-archive-keyring.gpg \
+    && echo "deb [signed-by=/usr/share/keyrings/mono-official-archive-keyring.gpg] https://download.mono-project.com/repo/debian stable-buster/snapshots/6.12.0.182 main" > /etc/apt/sources.list.d/mono-official-stable.list \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends mono-complete \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /opt/metaxtract
+
+COPY requirements-cli.txt ./
+RUN python3 -m venv /opt/venv \
+    && pip install --no-cache-dir --upgrade pip setuptools wheel \
+    && pip install --no-cache-dir -r requirements-cli.txt
+
+COPY . .
+
+ENTRYPOINT ["python", "/opt/metaxtract/main.py"]
+CMD ["--help"]