Add RStudio

RStudio/4.1.1/Dockerfile

+FROM rocker/rstudio:4.1.1
+
+LABEL CONTAINER_VERSION="0.0.2" \
+    AUTHOR="Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+# build-time varialbes
+ARG http_proxy=http://proxy.swmed.edu:3128/ 
+ARG https_proxy=http://proxy.swmed.edu:3128/ 
+ARG no_proxy="*.swmed.edu,*.swmed.org,*.utsouthwestern.edu,localhost,127.0.0.1/8"
+
+ENV http_proxy="${http_proxy}" \
+    https_proxy="${https_proxy}" \
+    no_proxy="${no_proxy}"
+
+RUN mkdir /vizapp
+
+# Allow root login. Ref. Section 3.2. https://s3.amazonaws.com/rstudio-server/rstudio-server-pro-0.99.903-admin-guide.pdf
+# Usefull for fakeroot function of singularity 
+RUN /usr/bin/bash -c "sed -i 's/^UID_MIN.*/UID_MIN                  0/g' /etc/login.defs"

RStudio/4.2.2/Dockerfile

+FROM rocker/rstudio:4.2.2
+
+LABEL CONTAINER_VERSION="0.0.2" \
+    AUTHOR="Peng Lian" \
+    EMAIL="biohpc-help@utsouthwestern.edu"
+
+# build-time varialbes
+ARG http_proxy=http://proxy.swmed.edu:3128/ 
+ARG https_proxy=http://proxy.swmed.edu:3128/ 
+ARG no_proxy="*.swmed.edu,*.swmed.org,*.utsouthwestern.edu,localhost,127.0.0.1/8"
+
+ENV http_proxy="${http_proxy}" \
+    https_proxy="${https_proxy}" \
+    no_proxy="${no_proxy}"
+
+RUN mkdir /vizapp
+
+# Allow root login. Ref. Section 3.2. https://s3.amazonaws.com/rstudio-server/rstudio-server-pro-0.99.903-admin-guide.pdf
+# Usefull for fakeroot function of singularity 
+RUN /usr/bin/bash -c "sed -i 's/^UID_MIN.*/UID_MIN                  0/g' /etc/login.defs"

RStudio/build_and_push.sh

+#!/bin/bash
+
+PACKAGE="rstudio"
+VERSION="$1"
+CONTAINER_TAG="${PACKAGE}:${VERSION}"
+CONTAINER_NAME="git.biohpc.swmed.edu:5050/astrocyte/container/${CONTAINER_TAG}"
+
+export DOCKER_BUILDKIT=0
+export COMPOSE_DOCKER_CLI_BUILD=0
+
+# build with proxy settings
+docker build -f ./${VERSION}/Dockerfile -t ${CONTAINER_TAG} ./${VERSION} &> build_and_push-${VERSION}.log
+
+# docker login
+# Please create your person "Acess token" and config the "~/.docker/config.json" to login automatically
+
+# Tag and push
+docker tag ${CONTAINER_TAG} ${CONTAINER_NAME}
+docker push ${CONTAINER_NAME}

RStudio/run_rstudio_singularity.sh

+#!/bin/bash
+#
+# This is an example script to demonstrate how to use an R container to install and run vizapp on a local host with docker.
+# root privilege is NOT required. 
+#
+# Author: Peng Lian
+#
+
+module load singularity/3.9.9
+
+tmpDir=/tmp/$USER/rstudio
+
+
+# vizapp folder on the host machine. (Will mount as /vizapp)
+VIZAPP_HOME="$tmpDir/vizapp/"
+
+# dependencies libs of vizapp, space seperated
+VIZAPP_LIBS="rmarkdown"
+
+# user specified path to install the vizapp libs inside the container
+R_LIBS_USER="/vizapp/rlibrary"
+
+# env of the vizapp. (Will mount to /mnt)
+outputDir=$(pwd)
+
+# prepare tmp and the library folder
+mkdir -p ${VIZAPP_HOME}/rlibrary
+mkdir -p $tmpDir/home
+mkdir -p $tmpDir/run
+mkdir -p $tmpDir/tmp
+
+chmod -R 777 $tmpDir &> /dev/null
+
+# build a soft link from outputDir (mounted as /mnt) to user's home
+ln -s /mnt $tmpDir/home/outputDir
+
+# version and the image to use
+PACKAGE="rstudio"
+VERSION="4.2.2"
+IMAGE_NAME="git.biohpc.swmed.edu:5050/astrocyte/container/${PACKAGE}:${VERSION}"
+
+# name of the local image
+singularity_image=${PACKAGE}_${VERSION}.sif
+
+# pull the container to a local image
+if [ ! -e ${singularity_image} ]; then
+    singularity pull ${singularity_image} docker://$IMAGE_NAME
+fi
+
+# Disable auth or not
+DISABLE_AUTH=true
+PASSWORD=BioHPC
+DEFAULT_USER=root
+
+# install vizapp libs to customize folder
+for lib in $VIZAPP_LIBS; do
+    SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
+    SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
+    SINGULARITYENV_PASSWORD=$PASSWORD \
+    SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+    singularity exec -f -C -w -e \
+    -H $tmpDir/home:/root \
+    -B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image} \
+    R -e "if (!require('$lib', character.only=TRUE)) {install.packages('$lib', dependencies=TRUE, lib='$R_LIBS_USER')}"
+done
+
+# run vizapp on localhost
+SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
+SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
+SINGULARITYENV_PASSWORD=$PASSWORD \
+SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+singularity run -f -C -w -e \
+-H $tmpDir/home:/root \
+-B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image}
+
+
+## Enable this section if run as non-root user inside the container
+## clean up the files created in the container
+#SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
+#SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
+#SINGULARITYENV_PASSWORD=$PASSWORD \
+#SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+#singularity exec -f -C -w -e \
+#-H $tmpDir/home:/root \
+#-B $tmpDir/run:/var/run,$tmpDir/tmp:/tmp ${singularity_image} \
+#/bin/bash -c "rm -fr /home/rstudio/* /home/rstudio/.* /var/run/* /tmp/* "
+
+# clean up tmp dir from host
+rm -fr $tmpDir