Merge branch 'master' of https://github.molgen.mpg.de/loosolab/wilson…

…-apps
loosolab · Mar 21, 2019 · 8fec4e70331499f2e6452265a41ff8267ce4c1f8 · 8fec4e7
2 parents abc62aa + 3b4f137
commit 8fec4e70331499f2e6452265a41ff8267ce4c1f8
Unified Split

Showing with 123 additions and 0 deletions.

+82 −0 docker/1.5.4/Dockerfile

+41 −0 docker/1.5.4/entrypoint.sh
diff --git a/docker/1.5.4/Dockerfile 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"]
diff --git a/docker/1.5.4/entrypoint.sh b/docker/1.5.4/entrypoint.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+#this script is run when the container is started
+#optionally adds $CONTAINERKEY to shiny server url by modifying shiny-server.conf
+#
+#example:
+#http://<IP>:<PORT>
+#->
+#http://<IP>:<PORT>/<CONTAINERKEY>
+#
+#to use this add the "-e" parameter when starting a container:
+#docker run ... -e CONTAINERKEY=${container_key} ...
+#example:
+#docker run --name='sav1' -d -p 50000:3838 -v '/mnt/agnerds/docker/projects/sav1':'/srv/shiny-server/data' -e CONTAINERKEY=sav1 loosolab/wilson:1.2"
+#-> http://<IP>:50000/sav1
+
+conf="/etc/shiny-server/shiny-server.conf"
+
+#create backup of original shiny-server.conf
+if [[ ! -f "${conf}.old" ]]; then
+	cp ${conf} ${conf}.old
+else
+	cp ${conf}.old ${conf}
+fi
+
+#add parameter(s) at top of .conf
+param="preserve_logs true;"
+sed -i "1i $param" ${conf}
+
+param="sanitize_errors off;"
+sed -i "1i $param" ${conf}
+
+#if environment variable given -> add key to url
+if [[ ! -z "$CONTAINERKEY" ]]; then
+	CONTAINERKEY=$(echo -e $CONTAINERKEY | sed 's/\//\\\//g')			#to escape "/"
+	cat ${conf} | sed "s/location \//location \/$CONTAINERKEY/g" >${conf}.1
+	mv ${conf}.1 ${conf}
+fi
+
+#start shiny server
+exec shiny-server 2>&1 >>/var/log/shiny-server.log