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1 # call parent container
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2 #FROM r4.0.0
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3 FROM debian:testing
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4
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5 # set author
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6 MAINTAINER Lain Pavot <lain.pavot@inra.fr>
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7
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8 # set encoding
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9 ENV LANG en_US.UTF-8
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10
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11 ## we copy the installer and run it before copying the entier project to prevent
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12 ## reinstalling everything each time the project has changed
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13
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14 COPY ./XSeeker/install.R /tmp/
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15
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16 RUN mkdir -p /XSeeker/input/ /var/log/
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17 VOLUME ["/XSeeker/input/"]
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18
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19 EXPOSE 8765
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20 ENV LC_ALL en_US.UTF-8
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21 ENV LANG en_US.UTF-8
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22 ENV R_BASE_VERSION 4.0.3
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23
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24 RUN \
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25 apt-get update \
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26 && apt-get install -y --no-install-recommends \
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27 ed \
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28 less \
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29 locales \
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30 vim-tiny \
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31 wget \
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32 ca-certificates \
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33 fonts-texgyre \
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34 && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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35 && locale-gen en_US.utf8 \
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36 && /usr/sbin/update-locale LANG=en_US.UTF-8 \
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37 && echo "deb http://http.debian.net/debian sid main" > \
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38 /etc/apt/sources.list.d/debian-unstable.list \
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39 && echo 'APT::Default-Release "testing";' > \
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40 /etc/apt/apt.conf.d/default \
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41 && echo 'APT::Install-Recommends "false";' > \
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42 /etc/apt/apt.conf.d/90local-no-recommends \
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43 && chmod o+r /etc/resolv.conf \
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44 && apt-get update \
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45 && apt-get install -y --no-install-recommends \
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46 file \
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47 gcc-9-base \
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48 libopenblas0-pthread \
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49 littler \
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50 libcurl4-openssl-dev \
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51 libxml2-dev \
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52 libssl-dev \
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53 libpwiz-dev \
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54 libpwiz3 \
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55 r-cran-littler \
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56 r-base \
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57 r-base-dev \
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58 r-recommended \
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59 r-cran-rlang \
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60 r-cran-dt \
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61 r-cran-magrittr \
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62 r-cran-ncdf4 \
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63 r-cran-devtools \
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64 r-cran-plotly \
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65 r-cran-httpuv \
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66 r-cran-xtable \
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67 r-cran-sourcetools \
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68 r-cran-fastmap \
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69 r-cran-rcurl \
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70 r-cran-proxy \
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71 r-cran-htmlwidgets \
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72 r-cran-rsqlite \
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73 r-cran-openxlsx \
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74 r-cran-stringr \
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75 r-cran-dplyr \
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76 r-cran-purrr \
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77 r-cran-blob \
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78 r-cran-dbscan \
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79 r-cran-biocmanager \
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80 r-bioc-biocgenerics \
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81 r-bioc-biobase \
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82 r-bioc-protgenerics \
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83 r-bioc-zlibbioc \
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84 && Rscript /tmp/install.R \
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85 && apt-get clean autoclean \
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86 && apt-get autoremove --yes \
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87 && rm -rf /var/lib/{apt,dpkg,cache,log}/ \
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88 && rm -rf /tmp/* ;
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89
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90 COPY ./XSeeker /XSeeker
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91 COPY ./XSeekerBaseModule /tmp/XSeekerBaseModule
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92
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93 COPY ./resources/XSeekerBaseModule/ /tmp/XSeekerBaseModule/
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94 COPY ./resources/XSeeker/config/ /XSeeker/config/
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95
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96 RUN \
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97 cd /tmp/XSeekerBaseModule \
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98 && ./configure \
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99 && make install \
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100 && cd /XSeeker \
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101 && ./configure \
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102 && make all_modules install \
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103 && rm -rf /tmp/XSeekerBaseModule/ ;
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104
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105
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106 RUN chmod +x /XSeeker/run.sh
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107
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108 COPY ./resources/entrypoint.sh /
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109 RUN chmod +x /entrypoint.sh
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110 CMD /entrypoint.sh
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