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comparison Dockerfile @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 7a6f2380fc1d
children
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8:1274e2a62479 9:0976a6257300
1 1
2 FROM python:3.10-buster 2 FROM python:3.9.12-slim-bullseye
3 3
4 # set author 4 # set author
5 MAINTAINER Ludovic Cottret <ludovic.cottret@inrae.fr> 5 LABEL maintainer "Ludovic Cottret <ludovic.cottret@inrae.fr>"
6 6
7 # set encoding 7 # set encoding
8 ENV LC_ALL en_US.UTF-8 8 ENV LC_ALL en_US.UTF-8
9 ENV LANG en_US.UTF-8 9 ENV LANG en_US.UTF-8
10 10
11 ENV PLANEMO_VENV_LOCATION /planemo-venv 11 ENV DEBIAN_FRONTEND=noninteractive
12 ENV CONDA /tmp/conda
13 12
14 RUN \ 13
15 apt-get update \ 14 RUN useradd -ms /bin/bash galaxy_user
16 && apt-get install -y --no-install-recommends \ 15 # RUN usermod -aG sudo galaxy_user
17 ed \ 16
18 less \ 17 # Install dependencies
19 locales \ 18 RUN apt-get update \
20 vim-tiny \ 19 && apt-get install -y \
21 wget \ 20 curl \
22 ca-certificates \ 21 sudo \
23 fonts-texgyre \ 22 build-essential \
24 build-essential \ 23 libseccomp-dev \
25 libseccomp-dev \ 24 autoconf \
26 pkg-config \ 25 automake \
27 squashfs-tools \ 26 cryptsetup \
28 cryptsetup \ 27 fuse2fs \
29 && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ 28 git \
30 && locale-gen en_US.utf8 \ 29 fuse \
31 && /usr/sbin/update-locale LANG=en_US.UTF-8 \ 30 libfuse-dev \
32 && echo "deb http://http.debian.net/debian buster main" > /etc/apt/sources.list.d/debian-unstable.list \ 31 libglib2.0-dev \
33 && echo 'APT::Default-Release "buster";' > /etc/apt/apt.conf.d/default \ 32 libseccomp-dev \
34 && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends \ 33 libtool \
35 && apt-get update \ 34 pkg-config \
36 && apt-get upgrade -y \ 35 runc \
37 && apt-get install -y --no-install-recommends \ 36 squashfs-tools \
38 git \ 37 squashfs-tools-ng \
39 littler \ 38 uidmap \
40 libhdf5-dev \ 39 wget \
41 python-virtualenv \ 40 zlib1g-dev
42 && pip install virtualenv \ 41
43 && python -m virtualenv "$PLANEMO_VENV_LOCATION" \ 42 # Install planemo
44 && . "$PLANEMO_VENV_LOCATION"/bin/activate \ 43 RUN pip install --upgrade pip \
45 && pip install --upgrade pip setuptools \ 44 && pip install planemo
46 && pip install planemo numpy \
47 && apt-get clean autoclean \
48 && apt-get autoremove --yes \
49 && rm -rf /var/lib/{apt,dpkg,cache,log}/ \
50 && rm -rf /usr/bin/X11 \
51 && rm -rf /tmp/*
52 45
53 SHELL ["/bin/bash", "-c"] 46 SHELL ["/bin/bash", "-c"]
54 47
48 # Install GO
55 RUN \ 49 RUN \
56 export VERSION=1.17.2 OS=linux ARCH=amd64 \ 50 export VERSION=1.17.2 OS=linux ARCH=amd64 \
57 && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ 51 && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \
58 && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ 52 && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \
59 && rm go$VERSION.$OS-$ARCH.tar.gz \ 53 && rm go$VERSION.$OS-$ARCH.tar.gz \
60 && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ 54 && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \
61 && source ~/.bashrc 55 && source ~/.bashrc
62 56
57 # Install Singularity
63 RUN \ 58 RUN \
64 echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ 59 echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \
65 && source ~/.bashrc \ 60 && source ~/.bashrc \
66 && export VERSION=3.10.0 \ 61 && export VERSION=3.10.0 \
67 && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ 62 && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \
68 && tar -xzf singularity-ce-${VERSION}.tar.gz \ 63 && tar -xzf singularity-ce-${VERSION}.tar.gz \
69 && cd singularity-ce-${VERSION} \ 64 && cd singularity-ce-${VERSION} \
70 && ./mconfig && \ 65 && ./mconfig \
71 make -C builddir && \ 66 && make -C builddir \
72 make -C builddir install 67 && make -C builddir install \
68 && cd .. \
69 && rm -rf singularity-ce-${VERSION} singularity-ce-${VERSION}.tar.gz
70
71 # Clean
72
73 RUN apt-get clean autoclean \
74 && apt-get autoremove --yes \
75 && rm -rf /var/lib/{apt,dpkg,cache,log}/ \
76 && rm -rf /usr/bin/X11 \
77 && rm -rf /tmp/*
78
79
80 # USER galaxyuser
73 81
74 CMD [] 82 CMD []
75 83