From 4689e0cb6224c2abf47bdf8b46c28a9be5cd59ab Mon Sep 17 00:00:00 2001
From: Carsten Kuenne <Carsten.kuenne@mpi-bn.mpg.de>
Date: Mon, 18 Mar 2019 14:12:10 +0100
Subject: [PATCH] Create Dockerfile

---
 docker/1.5.4/Dockerfile | 82 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 docker/1.5.4/Dockerfile

diff --git a/docker/1.5.4/Dockerfile b/docker/1.5.4/Dockerfile
new file mode 100644
index 0000000..2f86256
--- /dev/null
+++ b/docker/1.5.4/Dockerfile
@@ -0,0 +1,82 @@
+# Pulls debian:latest from dockerhub
+FROM debian
+
+# Dockerfile questions go to
+MAINTAINER C. Kuenne / MPI-BN / Bioinformatics / carsten.kuenne@mpi-bn.mpg.de
+
+#Some basic packages, updates and cleanup
+RUN apt-get -y update && apt-get -y upgrade && \
+apt-get -y install \
+r-base \
+wget \
+libnlopt-dev \
+libssl-dev \
+libxml2-dev \
+libcurl4-openssl-dev \
+git \
+procps \
+gdebi-core && \
+apt-get clean
+
+#Installs DEVTOOLS
+RUN Rscript -e "install.packages(c('devtools'), repos='https://cran.rstudio.com/')"
+
+#Installs BIOCONDUCTOR/BiocInstaller
+RUN Rscript -e 'source("https://bioconductor.org/biocLite.R")'
+
+#Install Shiny-Server
+#RUN wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb && \
+#gdebi -n shiny-server-1.5.6.875-amd64.deb && \
+#RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb && \
+#gdebi -n shiny-server-1.5.7.907-amd64.deb && \
+RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb && \
+gdebi -n shiny-server-1.5.9.923-amd64.deb && \
+rm /srv/shiny-server/index.html && \
+rm -rf /srv/shiny-server/sample-apps
+
+#install shinythemes
+RUN Rscript -e 'install.packages("shinythemes", repos="http://cran.wustl.edu/")'
+
+#install shinyBS
+RUN Rscript -e 'install.packages("shinyBS", repos="http://cran.wustl.edu/")'
+
+#install old mvtnorm package (1.0-8), because the current 1.0-10 needs r 3.5 (current debian r is 3.3)
+RUN Rscript -e 'devtools::install_version(repos="http://cran.wustl.edu/", package = "mvtnorm", version = "1.0-8")'
+
+#Install WILSON
+RUN Rscript -e 'devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3", auth_token = NULL, upgrade = "never")'
+
+#Install stackdump
+#RUN Rscript -e 'devtools::install_github(repo = "jcheng5/stackdump")'
+
+#Install WILSON App
+#RUN git clone -b stackdump https://github.molgen.mpg.de/loosolab/wilson-apps /srv/shiny-server/tmp && \
+RUN git clone https://github.molgen.mpg.de/loosolab/wilson-apps /srv/shiny-server/tmp && \
+cp -a /srv/shiny-server/tmp/wilson-basic/. /srv/shiny-server/ && \
+rm -rf /srv/shiny-server/tmp
+
+#Install webshot/phantomjs to permit download of interactive plots with plot.ly
+RUN Rscript -e 'install.packages("webshot", repos="http://cran.wustl.edu")'
+RUN Rscript -e 'webshot::install_phantomjs()'
+RUN cp /root/bin/phantomjs /usr/local/bin
+
+EXPOSE 3838
+
+RUN rm -rf /srv/shiny-server/data && \
+mkdir /srv/shiny-server/data
+
+#check current directory for the presence of clarion input files (*.se, *.clarion) -> include in container
+#add pointless additional copy of entrypoint.sh because otherwise the building will fail if no clarion files exist (yuck!)
+ADD entrypoint.sh *.se *.clarion /srv/shiny-server/data/
+RUN rm /srv/shiny-server/data/entrypoint.sh
+
+ADD entrypoint.sh /usr/bin/entrypoint.sh
+RUN chmod +x /usr/bin/entrypoint.sh
+
+#switch shiny user uid to 1000 (previously docker user); set permissions
+RUN usermod -u 1000 shiny && \
+chown -R shiny:shiny /srv/shiny-server/ && \
+mkdir -p /srv/shiny-server/logs && \
+chmod ugo+wrX /srv/shiny-server/logs
+
+CMD ["/usr/bin/entrypoint.sh"]