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# get shiny serves plus tidyverse packages image
#FROM rocker/shiny-verse:latest
#FROM ubuntu:18.04
FROM openanalytics/r-base:3.6.1
MAINTAINER "Justin Sing" github.com/singjc/DrawAlignR
## Make build no interactive
ARG DEBIAN_FRONTEND=noninteractive
ARG APT_KEY_DONT_WARN_ON_DANGEROUS_USEAGE=1
#######################
## System
#######################
RUN apt-get update && \
apt-get install -y software-properties-common && \
rm -rf /var/lib/apt/lists/*
#RUN apt-get update
#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
#RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/'
#RUN apt-get upate
# system libraries of general use
RUN apt-get update && apt-get install -y --no-install-recommends \
sudo \
build-essential \
gfortran \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev \
libnetcdf-dev \
libxml2-dev \
r-base \
python3.6 \
python3-pip \
python3-setuptools \
python3-dev &&\
mkdir -p /var/lib/shiny-server/bookmarks/shiny
#######################
## Python
#######################
# get python image
#FROM python:3.7.5-slim
# install required python modules
RUN pip3 install \
numpy \
pandas \
click \
pymsnumpress
#######################
## R language
#######################
# install R packages required
# (change it dependeing on the packages you need)
RUN R -e "install.packages('caTools')"
RUN R -e "install.packages('cowplot')"
RUN R -e "install.packages('xml2')"
RUN R -e "install.packages('roxygen2')"
RUN R -e "install.packages('rversions')"
RUN R -e "install.packages('devtools')"
#RUN R -e "install.packages('shiny', repos='http://cran.rstudio.com/')"
#RUN R -e "install.packages('shinyjs')"
#RUN R -e "install.packages('shinyBS')"
#RUN R -e "install.packages('shinyWidgets')"
##RUN R -e "install.packages('shinyFiles')"
#RUN R -e "install.packages('plotly')"
#RUN R -e "install.packages('parallel')"
#RUN R -e "devtools::install_github('singjc/mstools', force=T, upgrade='never')"
#RUN R -e "devtools::install_github('shubham1637/DIAlignR', upgrade='never')"
RUN R -e "library(devtools); devtools::install_github('singjc/DrawAlignR', force=T, build_opts = c('--no-build-vignettes'))"
# copy the app to the image
#COPY ./DrawAlignR.Rproj /srv/shiny-server/
#COPY ./inst/shiny-script/app.R /srv/shiny-server/
#COPY ./inst/shiny-script/external /srv/shiny-server/external/
#COPY ./inst/shiny-script/www /srv/shiny-server/www/
#COPY ./R /srv/shiny-server/R
#COPY ./inst/extdata/Synthetic_Dilution_Phosphoproteomics/ /srv/shiny-server/data/
COPY ./ /srv/shiny-server/DrawAlignR/
# select port
EXPOSE 3838
# Make all app files readable
RUN chmod -R +r /srv/shiny-server/DrawAlignR/
# allow permission
#RUN sudo chown -R shiny:shiny /srv/shiny-server/DrawAlignR/
# run app
CMD ["R", "-e", "shiny::runApp('/srv/shiny-server/DrawAlignR/inst/shiny-script/app.R', host='0.0.0.0', port=3838)"]