Mercurial > repos > jpayne > refchooser

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planemo upload commit 5080d34b4b5154190fb0c351ac20cd93ad156489
author galaxytrakr
date Mon, 16 Mar 2026 15:13:28 +0000
parents 719889ec4e14
children b23f76d954e5
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1 # =============================================================
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2 # Dockerfile for refchooser (compatible with Galaxy)
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3 # =============================================================
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5 # ---------- Build Stage 1: The "Builder" ----------
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6 # This stage downloads and prepares all our dependencies.
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7 FROM ubuntu:20.04 AS builder
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9 # Set versions for our tools to make updates easy.
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10 ARG MASH_VER="2.3"
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11 ARG PYTHON_VER="3.8"
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13 # Avoid interactive prompts during apt-get install.
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15 ENV DEBIAN_FRONTEND=noninteractive
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17 # Install all the dependencies needed to build our tools.
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18 RUN apt-get update && apt-get install -y --no-install-recommends \
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19 wget \
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20 tar \
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21 gzip \
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22 python${PYTHON_VER} \
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23 python${PYTHON_VER}-venv \
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24 && rm -rf /var/lib/apt/lists/*
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26 # Set a working directory for our downloads.
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27 WORKDIR /build
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29 # --- Install Mash ---
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30 # Download the pre-compiled Linux binary for Mash.
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31 ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
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32 # Unpack the tarball, find the 'mash' executable, and install it to a standard location.
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33 RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
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34 install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
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35
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36 # --- Install refchooser ---
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37 # Create a Python virtual environment in a standard location.
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38 RUN python${PYTHON_VER} -m venv /opt/venv
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39 # Activate the venv and install refchooser and its dependencies using pip.
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40 ENV PATH="/opt/venv/bin:$PATH"
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41 RUN pip install --no-cache-dir refchooser
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44 # ---------- Build Stage 2: The "Runtime" Stage ----------
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45 # This is our final, lean image that will be used by Galaxy.
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46 FROM ubuntu:20.04 AS runtime
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48 # Avoid interactive prompts.
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49 ENV DEBIAN_FRONTEND=noninteractive
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51 # Install only the essential runtime libraries needed by Mash and Python.
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52 RUN apt-get update && apt-get install -y --no-install-recommends \
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53 libgomp1 \
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54 python3.8-venv \
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55 && rm -rf /var/lib/apt/lists/*
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57 # --- Copy Binaries and Environment from Builder Stage ---
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59 # Copy the compiled 'mash' binary from the builder stage.
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60 COPY --from=builder /usr/local/bin/mash /usr/local/bin/mash
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62 # Copy the entire Python virtual environment containing 'refchooser'.
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63 COPY --from=builder /opt/venv /opt/venv
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65 # --- Final Configuration ---
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67 # Set the PATH environment variable so the system can find 'mash' and 'refchooser'.
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68 ENV PATH="/opt/venv/bin:$PATH"
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70 # As a best practice for Galaxy, ensure all users can read and execute the tools.
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71 RUN chmod -R a+rX /opt/venv && \
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72 chmod a+rx /usr/local/bin/mash
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74 # IMPORTANT: No ENTRYPOINT. Set a neutral CMD for Galaxy compatibility.
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75 CMD ["/bin/bash"]