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Dockerfile
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Dockerfile
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# datelifedocker
# Version: 0.5.0
# First, you have to choose and get a shiny image.
# Specifying "latest" on version did not work (it kept loading a very old R version).
# I had to specify explicitly the R version number, i.e., rocker/shiny:latest -> rocker/shiny:4.1.0
# FROM rocker/shiny:latest
FROM rocker/shiny:4.1.0
MAINTAINER Luna Sare <sanchez.reyes.luna@gmail.com>
# Install Linux system libraries of general use
RUN apt-get update && apt-get -y dist-upgrade
RUN apt-get install -y apt-utils \
software-properties-common \
libssl-dev \
libxml2-dev \
lib32z1-dev \
libblas-dev \
liblapack-dev \
libprotobuf-dev \
protobuf-compiler \
php libapache2-mod-php php-cli \
git-core \
curl \
wget \
libmagick++-dev libmagickcore-dev libmagickwand-dev \
libssh2-1-dev \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
xtail \
build-essential \
libglpk40
RUN R -e "R.Version()"
# Initialize git lfs
# git lfs, from https://github.com/git-lfs/git-lfs/wiki/Installation and debugging the libssh2-1-dev install first.
RUN apt install -y libssh-4 libssh-dev libssh2-1 libssh2-1-dev
RUN apt-get update && \
curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
apt-get install -y --no-install-recommends git-lfs && \
git lfs install && \
DEBIAN_FRONTEND=noninteractive apt-get purge -y --auto-remove ${build_deps} && \
rm -r /var/lib/apt/lists/*
# Install packages needed for the datelife shiny app to run
RUN R -e "update.packages(ask=FALSE)"
RUN R -e "install.packages(c('igraph', 'ggdag'))"
RUN R -e "install.packages(c('rcmdcheck', \
'shinycssloaders', \
'strap', \
'jsonlite', \
'stringr', \
'future', \
'phangorn', \
'latticeExtra', \
'Hmisc'))"
RUN R -e "install.packages(c('shiny', \
'shinydashboard', \
'lubridate', \
'magrittr', \
'glue', \
'DT', \
'devtools', \
'plotly'), repos='http://cran.rstudio.com/')"
RUN R -e "install.packages(c('bold', 'rotl', 'knitcitations', 'rentrez'), type='source')"
RUN R -e "devtools::install_github('fmichonneau/phylobase')" # regular install.packages command not working with phylobase; tried type = "source" and did not work either
RUN R -e "devtools::install_github('fmichonneau/phyloch')"
RUN R -e "devtools::install_github('phylotastic/rphylotastic')"
# Installing datelife from GitHub
# you can install form a dev branch, for example:
# RUN R -e "devtools::install_github('phylotastic/datelife', ref = 'datelife-plots')"
RUN R -e "devtools::install_github('phylotastic/datelife')"
RUN R -e "devtools::install_github('phylotastic/datelifeplot')"
# Installing PATHd8
RUN mkdir /usr/local/pathd8download && \
wget http://www2.math.su.se/PATHd8/PATHd8.zip -O /usr/local/pathd8download/PATHd8.zip && \
cd /usr/local/pathd8download && \
unzip /usr/local/pathd8download/PATHd8.zip && \
cc PATHd8.c -O3 -lm -o PATHd8 && \
cp PATHd8 /usr/local/bin/PATHd8
# Installing mrBayes
RUN apt-get update && \
apt-get install -y mrbayes
# Copying the datelifeweb shiny app to the docker image so it can be served
RUN apt-get update && \
cd /srv && \
pwd && \
rm -r /srv/shiny-server/* && \
git clone https://github.com/phylotastic/datelifeweb.git && \
mv /srv/datelifeweb/* /srv/shiny-server/
# select port
EXPOSE 80
CMD ["/usr/bin/shiny-server"]