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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
author mvdbeek
date Sun, 22 Jul 2018 13:37:34 -0400
parents cf6e2bba9714
children
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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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1 # Script runner base image
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2 #
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3 # VERSION 0.3
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4 # This Dockerfile is the base system for executing scripts with the docker scriptrunner.
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6 FROM toolshed/requirements
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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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10 # make sure the package repository is up to date
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11 ENV DEBIAN_FRONTEND noninteractive
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12 RUN apt-get -qq update
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14 # Install all requirements that are recommend by the Galaxy project
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15 RUN apt-get install -y --no-install-recommends bc imagemagick libfreetype6-dev wget curl \
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16 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev liblzma-dev \
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17 libpcre3-dev libbz2-dev libx11-dev
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18
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19 RUN mkdir /var/home && \
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20 useradd galaxy --create-home --home-dir /home/galaxy --uid 1450 && \
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21 chown -R galaxy:galaxy /home/galaxy/
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22 USER galaxy
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23 WORKDIR /home/galaxy
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24 ENV CONDA_PREFIX="/home/galaxy/conda" \
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25 PATH="/home/galaxy/conda/envs/default/bin:/home/galaxy/conda/bin:$PATH"
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27 RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh
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28 RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh
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29 RUN bash -c "conda create -y -q -c bioconda --name default samtools bcftools && \
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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30 conda config --add channels conda-forge && \
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31 conda config --add channels bioconda && \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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32 conda config --add channels iuc && \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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33 . activate default && \
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34 conda install ghostscript coreutils"
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35 USER root
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36 RUN chown -R galaxy:users /home/galaxy && \
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37 chmod g=rwx /home/galaxy && \
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38 usermod -G users galaxy