Mercurial > repos > lain > xseeker
changeset 1:0f3224a5adda draft
" master branch Updating"
| author | lain |
|---|---|
| date | Tue, 01 Feb 2022 14:28:08 +0000 |
| parents | 15c9fbefeaf1 |
| children | 85b4593da271 |
| files | Dockerfile.planemo Dockerfile.xseeker |
| diffstat | 2 files changed, 0 insertions(+), 165 deletions(-) [+] |
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--- a/Dockerfile.planemo Tue Feb 01 14:19:30 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ - -FROM python:3.8-buster - -# set author -MAINTAINER Lain Pavot <lain.pavot@inra.fr> - -# set encoding -ENV LC_ALL en_US.UTF-8 -ENV LANG en_US.UTF-8 - -ENV PLANEMO_VENV_LOCATION /planemo-venv -ENV CONDA /tmp/conda - -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 buster main" > /etc/apt/sources.list.d/debian-unstable.list \ - && echo 'APT::Default-Release "buster";' > /etc/apt/apt.conf.d/default \ - && echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90local-no-recommends \ - && apt-get update \ - && apt-get upgrade -y \ - && apt-get install -y --no-install-recommends \ - git \ - littler \ - libhdf5-dev \ - r-cran-littler \ - r-base \ - r-base-dev \ - r-recommended \ - python-virtualenv \ - && R -e 'install.packages("batch", repos="http://cran.us.r-project.org")' \ - && pip install virtualenv \ - && python -m virtualenv "$PLANEMO_VENV_LOCATION" \ - && . "$PLANEMO_VENV_LOCATION"/bin/activate \ - && pip install --upgrade pip setuptools \ - && pip install planemo numpy \ - && planemo conda_init --conda_prefix "$CONDA" \ - && apt-get clean autoclean \ - && apt-get autoremove --yes \ - && rm -rf /var/lib/{apt,dpkg,cache,log}/ \ - && rm -rf /usr/bin/X11 \ - && rm -rf /tmp/* ; - -CMD [] -
--- a/Dockerfile.xseeker Tue Feb 01 14:19:30 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -# 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