Mercurial > repos > mvdbeek > docker_scriptrunner

annotate dockerfiles/scriptrunner/Dockerfile @ 6:b28d3445992b draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
author mvdbeek
date Fri, 08 Jul 2016 17:31:44 -0400
parents e1f5be390bc3
children 77dca93454b7
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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
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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2 #
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3 # VERSION 0.3
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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4 # This Dockerfile is the base system for executing scripts with the docker scriptrunner.
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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6 FROM toolshed/requirements
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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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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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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14 # Install all requirements that are recommend by the Galaxy project
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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15 RUN apt-get install -y --no-install-recommends imagemagick libfreetype6-dev wget curl \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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16 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev liblzma-dev \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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17 libpcre3-dev libbz2-dev libx11-dev
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18
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b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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19 RUN mkdir /var/home && \
b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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20 useradd galaxy --create-home --home-dir /var/home/galaxy --uid 1450 && \
b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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21 chown -R galaxy:galaxy /var/home/galaxy/
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22 USER galaxy
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b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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23 WORKDIR /var/home/galaxy
b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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24 ENV CONDA_PREFIX="/var/home/galaxy/conda" \
b28d3445992b planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf
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25 PATH="/var/home/galaxy/conda/envs/default/bin:/var/home/galaxy/conda/bin:$PATH"
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b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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27 RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh
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28 RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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29 RUN bash -c "conda create -y -q -c bioconda --name default samtools==0.1.19 bcftools && \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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30 conda config --add channels r && \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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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 && \
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
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34 conda install ghostscript"
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e1f5be390bc3 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit a0b1360bc3e6b97f793caa1e6d60d8864308ee83
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35 USER root