# HG changeset patch
# User lain
# Date 1643725688 0
# Node ID 0f3224a5addaafd63d14271deb8911068d017d08
# Parent  15c9fbefeaf12c126982496f7345c49eb398cd00
" master branch Updating"

diff -r 15c9fbefeaf1 -r 0f3224a5adda Dockerfile.planemo
--- 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 []
-
diff -r 15c9fbefeaf1 -r 0f3224a5adda Dockerfile.xseeker
--- 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