Add more features to the run script

.gitignore

 *.log
 .history
 *.sif
+*.img

RStudio/run_rstudio_singularity.sh

@@ -8,87 +8,200 @@
 
 module load singularity/3.9.9
 
-tmpDir=/tmp/$USER/rstudio
+# Help function
+help-info(){
+cat << _EOF_
+Usage:
+    # run the container (default external library: ./library)
+    ./run_container.sh [-r/--run] [-l/--libfolder relative/path/to/the/library]
+
+    # prepare the outside libraries for the container (default external library: ./library)
+    ./run_container.sh -p/--prepare [-l/--libfolder relative/path/to/the/library] [-L/--libraries "libA libB libC"]
+
+    # show the help info
+    ./run_container.sh -h/--help
+_EOF_
+}
+
+# Get the parent path of this script
+SOURCE=${BASH_SOURCE[0]}
+while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+  SOURCE=$(readlink "$SOURCE")
+  [[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
 
 
-# vizapp folder on the host machine. (Will mount as /vizapp)
-VIZAPP_HOME="$tmpDir/vizapp/"
+# Image settings
+REPO="rstudio"
+TAG="4.2.2"
+IMAGE_NAME="git.biohpc.swmed.edu:5050/astrocyte/container/${REPO}:${TAG}"
 
-# dependencies libs of vizapp, space seperated
-#VIZAPP_LIBS="rmarkdown"
+# name of the local image
+singularity_image=${REPO}-${TAG}.img
 
-# user specified path to install the vizapp libs inside the container
-R_LIBS_USER="/vizapp/rlibrary"
+# pull the container to a local image
+if [ ! -e ${singularity_image} ]; then
+    singularity pull ${singularity_image} docker://$IMAGE_NAME
+fi
 
-# env of the vizapp. (Will mount to /mnt)
-outputDir=$(pwd)
+# vizapp folder on the host machine. (Will mount as /vizapp)
+VIZAPP_HOME="$DIR"
+
+# Prepare log file locations
+calling_username=$(id -un)
+host_name=$(hostname -s)
+tmpDir=/tmp/$USER/rstudio/$(date +%s)
 
-# prepare tmp and the library folder
-mkdir -p ${VIZAPP_HOME}/rlibrary
+rm -fr $tmpDir
 mkdir -p $tmpDir/home
 mkdir -p $tmpDir/run
 mkdir -p $tmpDir/tmp
-
-chmod -R 777 $tmpDir &> /dev/null
+chmod -R 777 $tmpDir
+chmod 700 $tmpDir
 
 # 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="4.1.1"
-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
+# env of the vizapp. (Will mount to /mnt)
+outputDir=${outputDir:-$(pwd)}
 
 # Disable auth or not
 DISABLE_AUTH=true
-PASSWORD=BioHPC
 DEFAULT_USER=root
 VIZAPP_PORT=8123
 
-# install vizapp libs to customize folder
-for lib in $VIZAPP_LIBS; do
+# Vizapp library folder refer to $VIZAPP_HOME, will be overrided by -l|--libfolder
+VIZAPP_LIBFOLDER="rlibrary"
+
+run_container(){
+
+    # Vizapp library folder on host
+    mkdir -p ${VIZAPP_HOME}/${VIZAPP_LIBFOLDER}
+
+    # user specified path to install the vizapp libs inside the container
+    R_LIBS_USER="/vizapp/${VIZAPP_LIBFOLDER}"
+
+    # mount and run
+    echo "Running the container with the following command ..."
+    cat <<_EOF_
     SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
     SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
-    SINGULARITYENV_PASSWORD=$PASSWORD \
     SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
     SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
-    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')}"
+    singularity run -f -C -w -e \
+        -H $tmpDir/home:/root \
+        -B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image}
+_EOF_
+
+    echo -e "\nPlease visit http://localhost:${VIZAPP_PORT} to connect to the RStudio server ...\n"
+
+    # run vizapp on localhost
+    SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
+    SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
+    SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+    SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
+    singularity run -f -C -w -e \
+        -H $tmpDir/home:/root \
+        -B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image}
+}
+
+# dependencies libs (space seperated), will be overrided by -L|--libraries
+VIZAPP_LIBS="rmarkdown"
+
+prepare_libs(){
+
+    # Vizapp library folder on host
+    mkdir -p ${VIZAPP_HOME}/${VIZAPP_LIBFOLDER}
+
+    # user specified path to install the vizapp libs inside the container
+    R_LIBS_USER="/vizapp/${VIZAPP_LIBFOLDER}"
+
+    echo "Start to install libs \"${VIZAPP_LIBS}\" to \"${VIZAPP_HOME}/${VIZAPP_LIBFOLDER}\" ..."
+
+    # install vizapp libs to customize folder
+    for lib in $VIZAPP_LIBS; do
+        SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
+        SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
+        SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+        SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
+        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
+
+}
+
+
+# Default option settings
+POSITIONAL_ARGS=()
+LIBFOLDER="library"   # A folder inside $VIZAPP_HOME
+
+# Capture the options and positional argument
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -p|--prepare)
+      PREPARE="YES"
+      shift # past argument
+      ;;
+    -r|--run)
+      RUN="YES"
+      shift # past argument
+      ;;
+    -L|--libraries)
+      LIBS="$2"
+      shift
+      shift
+      ;;
+    -l|--libfolder)
+      LIBFOLDER="$2"
+      shift
+      shift
+      ;;
+    -*|--*)
+      help-info
+      exit 1
+      ;;
+    *)
+      POSITIONAL_ARGS+=("$1") # save positional arg
+      shift # past argument
+      ;;
+  esac
 done
+set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters
+
+
+# Determine how to run this script
+if [[ -z $PREPARE && -z $RUN  && -z $POSITIONAL_ARGS ]]; then
+    echo "Running the container with lib \"$LIBFOLDER\" ..."
+    VIZAPP_LIBFOLDER=$LIBFOLDER
+    run_container
+    # clean up tmp dir from host
+    rm -fr $tmpDir
+elif [[ $PREPARE == "YES" && $RUN == "YES" ]]; then
+    echo "Preparing the libraries with lib \"$LIBFOLDER\" ..."
+    VIZAPP_LIBFOLDER=$LIBFOLDER
+    VIZAPP_LIBS=$LIBS
+    prepare_libs
+
+    echo "Running the container with lib \"$LIBFOLDER\" ..."
+    run_container
+    # clean up tmp dir from host
+    rm -fr $tmpDir
+elif [[ $PREPARE == "YES" ]]; then
+    echo "Preparing the libraries with lib \"$LIBFOLDER\" ..."
+    VIZAPP_LIBFOLDER=$LIBFOLDER
+    VIZAPP_LIBS=$LIBS
+    prepare_libs
+elif [[ $RUN == "YES"  ]]; then
+    echo "Running the container with lib \"$LIBFOLDER\" ..."
+    VIZAPP_LIBFOLDER=$LIBFOLDER
+    run_container
+    # clean up tmp dir from host
+    rm -fr $tmpDir
+else
+    help-info
+fi
 
-echo -e "\nPlease visit http://localhost:${VIZAPP_PORT} to connect to the RStudio server ...\n"
-
-# run vizapp on localhost
-SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
-SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
-SINGULARITYENV_PASSWORD=$PASSWORD \
-SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
-SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
-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