Mercurial > repos > metexplore > met4j
diff Dockerfile @ 9:0976a6257300 draft
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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--- a/Dockerfile Wed Jul 26 15:33:45 2023 +0000 +++ b/Dockerfile Fri Jan 31 18:28:53 2025 +0000 @@ -1,75 +1,83 @@ -FROM python:3.10-buster +FROM python:3.9.12-slim-bullseye # set author -MAINTAINER Ludovic Cottret <ludovic.cottret@inrae.fr> +LABEL maintainer "Ludovic Cottret <ludovic.cottret@inrae.fr>" # set encoding ENV LC_ALL en_US.UTF-8 ENV LANG en_US.UTF-8 -ENV PLANEMO_VENV_LOCATION /planemo-venv -ENV CONDA /tmp/conda +ENV DEBIAN_FRONTEND=noninteractive + + +RUN useradd -ms /bin/bash galaxy_user +# RUN usermod -aG sudo galaxy_user -RUN \ - apt-get update \ - && apt-get install -y --no-install-recommends \ - ed \ - less \ - locales \ - vim-tiny \ - wget \ - ca-certificates \ - fonts-texgyre \ - build-essential \ - libseccomp-dev \ - pkg-config \ - squashfs-tools \ - cryptsetup \ - && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ - && locale-gen en_US.utf8 \ - && /usr/sbin/update-locale LANG=en_US.UTF-8 \ - && echo "deb http://http.debian.net/debian buster main" > /etc/apt/sources.list.d/debian-unstable.list \ - && echo 'APT::Default-Release "buster";' > /etc/apt/apt.conf.d/default \ - && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends \ - && apt-get update \ - && apt-get upgrade -y \ - && apt-get install -y --no-install-recommends \ - git \ - littler \ - libhdf5-dev \ - python-virtualenv \ - && pip install virtualenv \ - && python -m virtualenv "$PLANEMO_VENV_LOCATION" \ - && . "$PLANEMO_VENV_LOCATION"/bin/activate \ - && pip install --upgrade pip setuptools \ - && pip install planemo numpy \ - && apt-get clean autoclean \ - && apt-get autoremove --yes \ - && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ - && rm -rf /usr/bin/X11 \ - && rm -rf /tmp/* +# Install dependencies +RUN apt-get update \ + && apt-get install -y \ + curl \ + sudo \ + build-essential \ + libseccomp-dev \ + autoconf \ + automake \ + cryptsetup \ + fuse2fs \ + git \ + fuse \ + libfuse-dev \ + libglib2.0-dev \ + libseccomp-dev \ + libtool \ + pkg-config \ + runc \ + squashfs-tools \ + squashfs-tools-ng \ + uidmap \ + wget \ + zlib1g-dev + +# Install planemo +RUN pip install --upgrade pip \ + && pip install planemo SHELL ["/bin/bash", "-c"] +# Install GO RUN \ - export VERSION=1.17.2 OS=linux ARCH=amd64 \ - && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ - && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ - && rm go$VERSION.$OS-$ARCH.tar.gz \ - && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ + export VERSION=1.17.2 OS=linux ARCH=amd64 \ + && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ + && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ + && rm go$VERSION.$OS-$ARCH.tar.gz \ + && echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ && source ~/.bashrc +# Install Singularity RUN \ echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc \ && source ~/.bashrc \ - && export VERSION=3.10.0 \ - && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ - && tar -xzf singularity-ce-${VERSION}.tar.gz \ + && export VERSION=3.10.0 \ + && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ + && tar -xzf singularity-ce-${VERSION}.tar.gz \ && cd singularity-ce-${VERSION} \ - && ./mconfig && \ - make -C builddir && \ - make -C builddir install + && ./mconfig \ + && make -C builddir \ + && make -C builddir install \ + && cd .. \ + && rm -rf singularity-ce-${VERSION} singularity-ce-${VERSION}.tar.gz + +# Clean + +RUN apt-get clean autoclean \ + && apt-get autoremove --yes \ + && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ + && rm -rf /usr/bin/X11 \ + && rm -rf /tmp/* + + +# USER galaxyuser CMD []