Mercurial > repos > jpayne > refchooser

comparison Dockerfile @ 2:719889ec4e14 draft

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planemo upload commit 92689f52a93241194941ecf374629245c8fb9093
author galaxytrakr
date Mon, 16 Mar 2026 15:02:07 +0000
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1:dcf6c2409ebb 2:719889ec4e14
1 # =============================================================
2 # Dockerfile for refchooser (compatible with Galaxy)
3 # =============================================================
4
5 # ---------- Build Stage 1: The "Builder" ----------
6 # This stage downloads and prepares all our dependencies.
7 FROM ubuntu:20.04 AS builder
8
9 # Set versions for our tools to make updates easy.
10 ARG MASH_VER="2.3"
11 ARG PYTHON_VER="3.8"
12
13 # Avoid interactive prompts during apt-get install.
14 ENV DEBIAN_FRONTEND=noninteractive
15
16 # Install all the dependencies needed to build our tools.
17 RUN apt-get update && apt-get install -y --no-install-recommends \
18 wget \
19 tar \
20 gzip \
21 python${PYTHON_VER} \
22 python${PYTHON_VER}-venv \
23 && rm -rf /var/lib/apt/lists/*
24
25 # Set a working directory for our downloads.
26 WORKDIR /build
27
28 # --- Install Mash ---
29 # Download the pre-compiled Linux binary for Mash.
30 ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
31 # Unpack the tarball, find the 'mash' executable, and install it to a standard location.
32 RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
33 install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
34
35 # --- Install refchooser ---
36 # Create a Python virtual environment in a standard location.
37 RUN python${PYTHON_VER} -m venv /opt/venv
38 # Activate the venv and install refchooser and its dependencies using pip.
39 ENV PATH="/opt/venv/bin:$PATH"
40 RUN pip install --no-cache-dir refchooser
41
42
43 # ---------- Build Stage 2: The "Runtime" Stage ----------
44 # This is our final, lean image that will be used by Galaxy.
45 FROM ubuntu:20.04 AS runtime
46
47 # Avoid interactive prompts.
48 ENV DEBIAN_FRONTEND=noninteractive
49
50 # Install only the essential runtime libraries needed by Mash and Python.
51 RUN apt-get update && apt-get install -y --no-install-recommends \
52 libgomp1 \
53 python3.8-venv \
54 && rm -rf /var/lib/apt/lists/*
55
56 # --- Copy Binaries and Environment from Builder Stage ---
57
58 # Copy the compiled 'mash' binary from the builder stage.
59 COPY --from=builder /usr/local/bin/mash /usr/local/bin/mash
60
61 # Copy the entire Python virtual environment containing 'refchooser'.
62 COPY --from=builder /opt/venv /opt/venv
63
64 # --- Final Configuration ---
65
66 # Set the PATH environment variable so the system can find 'mash' and 'refchooser'.
67 ENV PATH="/opt/venv/bin:$PATH"
68
69 # As a best practice for Galaxy, ensure all users can read and execute the tools.
70 RUN chmod -R a+rX /opt/venv && \
71 chmod a+rx /usr/local/bin/mash
72
73 # IMPORTANT: No ENTRYPOINT. Set a neutral CMD for Galaxy compatibility.
74 CMD ["/bin/bash"]