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planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
author goeckslab
date Tue, 09 Dec 2025 23:49:47 +0000
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-1:000000000000 0:375c36923da1
1 FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04
2
3 ENV DEBIAN_FRONTEND=noninteractive
4 ENV NVIDIA_VISIBLE_DEVICES=all
5 ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility
6
7 # Install system dependencies, Python, and Chromium bits needed for Kaleido
8 RUN apt-get update && apt-get install -y --no-install-recommends \
9 python3 \
10 python3-pip \
11 python3-dev \
12 python3-venv \
13 ca-certificates \
14 build-essential \
15 gnupg \
16 libblas-dev \
17 liblapack-dev \
18 libgomp1 \
19 libopenblas-dev \
20 unzip \
21 pkg-config \
22 libfreetype6-dev \
23 libpng-dev \
24 libqhull-dev \
25 fonts-liberation \
26 libasound2 \
27 libatk-bridge2.0-0 \
28 libatk1.0-0 \
29 libcairo2 \
30 libcups2 \
31 libdbus-1-3 \
32 libexpat1 \
33 libfontconfig1 \
34 libgbm1 \
35 libgcc1 \
36 libglib2.0-0 \
37 libgtk-3-0 \
38 libnspr4 \
39 libnss3 \
40 libpango-1.0-0 \
41 libpangocairo-1.0-0 \
42 libstdc++6 \
43 libx11-6 \
44 libx11-xcb1 \
45 libxcb1 \
46 libxcomposite1 \
47 libxcursor1 \
48 libxdamage1 \
49 libxext6 \
50 libxfixes3 \
51 libxi6 \
52 libxrandr2 \
53 libxrender1 \
54 libxtst6 \
55 lsb-release \
56 wget \
57 xdg-utils \
58 && ln -sf /usr/bin/python3 /usr/bin/python \
59 && ln -sf /usr/bin/pip3 /usr/bin/pip \
60 && rm -rf /var/lib/apt/lists/*
61
62 # Pin setuptools <81 to avoid pkg_resources warnings and upgrade pip/wheel
63 RUN pip install --no-cache-dir 'setuptools<81.0.0' && \
64 pip install --no-cache-dir --upgrade pip wheel
65
66 # Install GPU-enabled PyTorch stack before AutoGluon so it picks up CUDA
67 RUN pip install --no-cache-dir \
68 --index-url https://download.pytorch.org/whl/cu118 \
69 --extra-index-url https://pypi.org/simple \
70 torch==2.1.2 \
71 torchvision==0.16.2 \
72 torchaudio==2.1.2
73
74 # Core Python dependencies
75 RUN pip install --no-cache-dir \
76 autogluon==1.4.0 \
77 pyarrow==20.0.0 \
78 matplotlib \
79 seaborn \
80 shap
81
82 # Update kaleido for plotting support
83 RUN pip install --no-cache-dir --upgrade kaleido
84
85 RUN apt-get update && apt-get install -y curl \
86 && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
87 && apt-get install -y nodejs \
88 && npm install -g yarn \
89 && rm -rf /var/lib/apt/lists/*