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1 ################################################################################
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2 ###
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3 ### [CONTAINER CORE FUNCTIONS]:
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4 ### install "Tool - Generic Filter" Galaxy tool (and required third part softwares, libraries, ...).
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5 ### [NOTE]
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6 ### please refer to README.md and about_docker.md files for further informations
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7 ###
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8 ################################################################################
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9
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10 ################################################################################
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11 ### fix parent containter
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12 FROM ubuntu:16.04
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13
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14 ################################################################################
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15 ### set author
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16 MAINTAINER Nils Paulhe <nils.paulhe@inra.fr>
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17
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18 ################################################################################
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19 ### sets the environment variables
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20 ENV TOOL_VERSION = "release_2016.03.03"
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21 ENV CONTAINER_VERSION = 0.1
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22
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23 LABEL version = "${CONTAINER_VERSION}"
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24 LABEL tool_version = "${TOOL_VERSION}"
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25
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26 ################################################################################
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27 ### install third part tools
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28
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29 # add debian repo for latest version of R
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30 RUN echo "deb http://cran.univ-paris1.fr/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list && \
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31 apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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32
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33 # Update and upgrade system
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34 RUN apt-get update && \
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35 apt-get -y upgrade
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36
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37 # install R
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38 RUN apt-get install -y \
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39 r-base \
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40 libcurl4-openssl-dev \
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41 libxml2-dev
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42 # NOTE: add `apt-get install -y git` if required
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43
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44 # init R env. (Docker)
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45 RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
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46
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47 # install R libs
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48 RUN Rscript -e "install.packages('batch', dep=TRUE)"
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49
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50 ################################################################################
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51 ### install core scripts
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52
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53 # init. WORKDIR
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54 RUN [ "mkdir", "/scripts" ]
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55
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56 #
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57 # [NOTE] to add scripts, we have two options: get them from GitHub OR copy them from this directory
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58 #
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59
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60 # get scripts using Git (option 1)
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61 # RUN cd /scripts && \
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62 # git clone -b release/${TOOL_VERSION} --recursive https://github.com/workflow4metabolomics/tool-generic_filter.git
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63
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64 # copy scripts files from this directory (option 2)
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65 COPY "." "/scripts/"
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66
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67 ## set WORKDIR
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68 # WORKDIR "/scripts"
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69
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70 # set authorizations
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71 RUN ["chmod", "a+x", "/scripts/filter_wrap.R"]
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72
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73 # make tool accessible through PATH
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74 ENV PATH = $PATH:/scripts
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75
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76 ################################################################################
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77 ### clean
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78 RUN apt-get clean && \
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79 apt-get autoremove -y && \
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80 rm -rf /var/lib/{apt,dpkg,cache,log}/ /tmp/* /var/tmp/*
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81 # NOTE: run `apt-get remove -y git && \` if required
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82
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83 ################################################################################
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84 ### Define Entry point script
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85 ## ENTRYPOINT ["/scripts/filter_wrap.R"]
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86
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87 ### [END] |
