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comparison Dockerfile.xseeker @ 0:15c9fbefeaf1 draft

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" master branch Updating"
author lain
date Tue, 01 Feb 2022 14:19:30 +0000
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-1:000000000000 0:15c9fbefeaf1
1 # call parent container
2 #FROM r4.0.0
3 FROM debian:testing
4
5 # set author
6 MAINTAINER Lain Pavot <lain.pavot@inra.fr>
7
8 # set encoding
9 ENV LANG en_US.UTF-8
10
11 ## we copy the installer and run it before copying the entier project to prevent
12 ## reinstalling everything each time the project has changed
13
14 COPY ./XSeeker/install.R /tmp/
15
16 RUN mkdir -p /XSeeker/input/ /var/log/
17 VOLUME ["/XSeeker/input/"]
18
19 EXPOSE 8765
20 ENV LC_ALL en_US.UTF-8
21 ENV LANG en_US.UTF-8
22 ENV R_BASE_VERSION 4.0.3
23
24 RUN \
25 apt-get update \
26 && apt-get install -y --no-install-recommends \
27 ed \
28 less \
29 locales \
30 vim-tiny \
31 wget \
32 ca-certificates \
33 fonts-texgyre \
34 && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
35 && locale-gen en_US.utf8 \
36 && /usr/sbin/update-locale LANG=en_US.UTF-8 \
37 && echo "deb http://http.debian.net/debian sid main" > \
38 /etc/apt/sources.list.d/debian-unstable.list \
39 && echo 'APT::Default-Release "testing";' > \
40 /etc/apt/apt.conf.d/default \
41 && echo 'APT::Install-Recommends "false";' > \
42 /etc/apt/apt.conf.d/90local-no-recommends \
43 && chmod o+r /etc/resolv.conf \
44 && apt-get update \
45 && apt-get install -y --no-install-recommends \
46 file \
47 gcc-9-base \
48 libopenblas0-pthread \
49 littler \
50 libcurl4-openssl-dev \
51 libxml2-dev \
52 libssl-dev \
53 libpwiz-dev \
54 libpwiz3 \
55 r-cran-littler \
56 r-base \
57 r-base-dev \
58 r-recommended \
59 r-cran-rlang \
60 r-cran-dt \
61 r-cran-magrittr \
62 r-cran-ncdf4 \
63 r-cran-devtools \
64 r-cran-plotly \
65 r-cran-httpuv \
66 r-cran-xtable \
67 r-cran-sourcetools \
68 r-cran-fastmap \
69 r-cran-rcurl \
70 r-cran-proxy \
71 r-cran-htmlwidgets \
72 r-cran-rsqlite \
73 r-cran-openxlsx \
74 r-cran-stringr \
75 r-cran-dplyr \
76 r-cran-purrr \
77 r-cran-blob \
78 r-cran-dbscan \
79 r-cran-biocmanager \
80 r-bioc-biocgenerics \
81 r-bioc-biobase \
82 r-bioc-protgenerics \
83 r-bioc-zlibbioc \
84 && Rscript /tmp/install.R \
85 && apt-get clean autoclean \
86 && apt-get autoremove --yes \
87 && rm -rf /var/lib/{apt,dpkg,cache,log}/ \
88 && rm -rf /tmp/* ;
89
90 COPY ./XSeeker /XSeeker
91 COPY ./XSeekerBaseModule /tmp/XSeekerBaseModule
92
93 COPY ./resources/XSeekerBaseModule/ /tmp/XSeekerBaseModule/
94 COPY ./resources/XSeeker/config/ /XSeeker/config/
95
96 RUN \
97 cd /tmp/XSeekerBaseModule \
98 && ./configure \
99 && make install \
100 && cd /XSeeker \
101 && ./configure \
102 && make all_modules install \
103 && rm -rf /tmp/XSeekerBaseModule/ ;
104
105
106 RUN chmod +x /XSeeker/run.sh
107
108 COPY ./resources/entrypoint.sh /
109 RUN chmod +x /entrypoint.sh
110 CMD /entrypoint.sh