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Better readability of Dockerfile, fix editing of userid for Dockerfile in DockerToolFactory.py.
author mvdbeek
date Wed, 03 Dec 2014 00:26:43 +0100
parents 7e0392d4531c
children 477eac6c4cea
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1 # Toolfactory image
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2 #
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3 # VERSION 0.1
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4 # This Dockerfile is the base system for executing scripts by the DockerToolFactory.
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6 FROM debian:jessie
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8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
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9
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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 --no-install-recommends -y autoconf automake build-essential gfortran \
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16 cmake git-core libatlas-base-dev libblas-dev liblapack-dev mercurial subversion python-dev \
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17 pkg-config openjdk-7-jre python-setuptools adduser zlib1g-dev ghostscript r-base-core \
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18 graphicsmagick-imagemagick-compat
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20 RUN apt-get install -y python-virtualenv libfreetype6-dev exonerate bedtools wget curl \
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21 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \
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22 libpcre3-dev libbz2-dev
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24 RUN easy_install pip
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26 RUN pip install numpy pysam tornado matplotlib pip pandas ipython rpy2
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28 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")'
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29 RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'
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31 #add galaxy user (could be any username).
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32 #1001 will be replaced by the actual user id of the system user
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33 #executing the galaxy tool, so that file write operations are possible.
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34 RUN adduser galaxy -u 1001
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36 #VOLUME ["/home/galaxy/"]
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37 RUN mkdir /home/galaxy/job_working_directory
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38 WORKDIR /home/galaxy/job_working_directory
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39 USER galaxy
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42 #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy
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43 CMD /bin/bash