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Initial Commit.
author m.vandenbeek@gmail.com
date Tue, 02 Dec 2014 15:14:12 +0100
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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
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5 FROM debian:jessie
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6
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7 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
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8
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9 # make sure the package repository is up to date
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10 RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update
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11
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12 # Install all requirements that are recommend by the Galaxy project
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13 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf
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14 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake
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15 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential
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16 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran
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17 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake
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18 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core
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19 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev
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20 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev
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21 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev
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22 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial
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23 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion
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24 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev
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25 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config
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26 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre
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27 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools
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28 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y adduser
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29 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y python-virtualenv
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30 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y zlib1g-dev
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31 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libfreetype6-dev
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32 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y ghostscript
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33 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base-core
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34 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y imagemagick
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35 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y graphicsmagick-imagemagick-compat
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36 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y exonerate
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37 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y bedtools
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38 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget
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39 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y curl
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40 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev
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41 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libssl-dev
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42 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libreadline-dev
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43 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libxml2-dev
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44 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools
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45
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46 RUN DEBIAN_FRONTEND=noninteractive easy_install numpy
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47 RUN DEBIAN_FRONTEND=noninteractive easy_install pysam
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48 RUN DEBIAN_FRONTEND=noninteractive easy_install tornado
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49 RUN DEBIAN_FRONTEND=noninteractive easy_install matplotlib
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50 RUN DEBIAN_FRONTEND=noninteractive easy_install pycurl
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51 RUN DEBIAN_FRONTEND=noninteractive easy_install pip
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52 RUN DEBIAN_FRONTEND=noninteractive pip install metaseq
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53 RUN DEBIAN_FRONTEND=noninteractive easy_install pandas
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54 RUN DEBIAN_FRONTEND=noninteractive pip install ipython
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55 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y zlib1g-dev
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56 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y liblzma-dev
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57 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libpcre3-dev
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58 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libbz2-dev
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59 RUN DEBIAN_FRONTEND=noninteractive pip install rpy2
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60
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61 RUN Rscript -e 'install.packages("latticeExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")'
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62 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")'
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63 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq")'
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64 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR")'
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65 RUN Rscript -e 'install.packages("ggplot2", dependencies=TRUE, repos="http://cran.us.r-project.org")'
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66 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("EDASeq")'
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67 RUN Rscript -e 'install.packages("reshape", dependencies=TRUE, repos="http://cran.us.r-project.org")'
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68 RUN Rscript -e 'install.packages("gridExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")'
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69
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70
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71 RUN adduser galaxy -u 1002
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72
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73 #VOLUME ["/home/galaxy/"]
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74 #RUN chown -R galaxy /home/galaxy/ ##Doesn't work on volumes
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75 RUN mkdir /home/galaxy/job_working_directory
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76 WORKDIR /home/galaxy/job_working_directory
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77 USER galaxy
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78
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79
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80 #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy
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81 CMD /bin/bash