Mercurial > repos > lain > xseeker
diff Dockerfile.xseeker @ 0:15c9fbefeaf1 draft
" master branch Updating"
| author | lain |
|---|---|
| date | Tue, 01 Feb 2022 14:19:30 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile.xseeker Tue Feb 01 14:19:30 2022 +0000 @@ -0,0 +1,110 @@ +# call parent container +#FROM r4.0.0 +FROM debian:testing + +# set author +MAINTAINER Lain Pavot <lain.pavot@inra.fr> + +# set encoding +ENV LANG en_US.UTF-8 + +## we copy the installer and run it before copying the entier project to prevent +## reinstalling everything each time the project has changed + +COPY ./XSeeker/install.R /tmp/ + +RUN mkdir -p /XSeeker/input/ /var/log/ +VOLUME ["/XSeeker/input/"] + +EXPOSE 8765 +ENV LC_ALL en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV R_BASE_VERSION 4.0.3 + +RUN \ + apt-get update \ + && apt-get install -y --no-install-recommends \ + ed \ + less \ + locales \ + vim-tiny \ + wget \ + ca-certificates \ + fonts-texgyre \ + && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ + && locale-gen en_US.utf8 \ + && /usr/sbin/update-locale LANG=en_US.UTF-8 \ + && echo "deb http://http.debian.net/debian sid main" > \ + /etc/apt/sources.list.d/debian-unstable.list \ + && echo 'APT::Default-Release "testing";' > \ + /etc/apt/apt.conf.d/default \ + && echo 'APT::Install-Recommends "false";' > \ + /etc/apt/apt.conf.d/90local-no-recommends \ + && chmod o+r /etc/resolv.conf \ + && apt-get update \ + && apt-get install -y --no-install-recommends \ + file \ + gcc-9-base \ + libopenblas0-pthread \ + littler \ + libcurl4-openssl-dev \ + libxml2-dev \ + libssl-dev \ + libpwiz-dev \ + libpwiz3 \ + r-cran-littler \ + r-base \ + r-base-dev \ + r-recommended \ + r-cran-rlang \ + r-cran-dt \ + r-cran-magrittr \ + r-cran-ncdf4 \ + r-cran-devtools \ + r-cran-plotly \ + r-cran-httpuv \ + r-cran-xtable \ + r-cran-sourcetools \ + r-cran-fastmap \ + r-cran-rcurl \ + r-cran-proxy \ + r-cran-htmlwidgets \ + r-cran-rsqlite \ + r-cran-openxlsx \ + r-cran-stringr \ + r-cran-dplyr \ + r-cran-purrr \ + r-cran-blob \ + r-cran-dbscan \ + r-cran-biocmanager \ + r-bioc-biocgenerics \ + r-bioc-biobase \ + r-bioc-protgenerics \ + r-bioc-zlibbioc \ + && Rscript /tmp/install.R \ + && apt-get clean autoclean \ + && apt-get autoremove --yes \ + && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ + && rm -rf /tmp/* ; + +COPY ./XSeeker /XSeeker +COPY ./XSeekerBaseModule /tmp/XSeekerBaseModule + +COPY ./resources/XSeekerBaseModule/ /tmp/XSeekerBaseModule/ +COPY ./resources/XSeeker/config/ /XSeeker/config/ + +RUN \ + cd /tmp/XSeekerBaseModule \ + && ./configure \ + && make install \ + && cd /XSeeker \ + && ./configure \ + && make all_modules install \ + && rm -rf /tmp/XSeekerBaseModule/ ; + + +RUN chmod +x /XSeeker/run.sh + +COPY ./resources/entrypoint.sh / +RUN chmod +x /entrypoint.sh +CMD /entrypoint.sh