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Singularity run command updated
#3 to fix Singularity container run, we added a bash script and 'how to run' details on README.
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‎README.md

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@@ -79,9 +79,6 @@ We provide Docker container for local use. Please note, the docker container was
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```
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# with docker container
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docker run --rm -p 3838:3838 jd21/methylr:latest
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# with singularity container
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singularity run docker://jd21/methylr:latest
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```
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##### Step:2 - web-browser
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http://localhost:3838
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```
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**For Singularity container**
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Thanks to WiilieYu (https://github.com/JD2112/methylr/issues/3), we found a problem on running Singularity/Apptainer container on methylR and using a script from [sigularity-shiny](https://github.com/vsoch/singularity-shiny), we solved the issue. Please run the commands below for Singularity container (tested with Singularity v3.8.6) -
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1. To run the [Singularity](https://docs.sylabs.io/guides/latest/user-guide/) or [Apptainer](https://apptainer.org/docs/user/main/index.html), please use the following commandlines -
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```
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# Copy prepare_template.sh to <YOUR_LOCAL_PATH> and run
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/bin/bash prepare_template.sh start
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```
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The above command run will generate an script on the terminal and command to run on the server,
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```
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$ /bin/bash prepare_template.sh start
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Generating shiny configuration...
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port: 15910 # PLEASE NOTE THIS WILL BE CHANGED IN YOUR COMPUTER
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logs: /tmp/shiny-server.ie3djR
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base: /srv/shiny-server
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run_as: jyotirmoy #<YOUR_USER_NAME>
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Server logging will be in /tmp/shiny-server.ie3djR
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To run your server:
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singularity run --bind /tmp/shiny-server.ie3djR/logs:/var/log/shiny \
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--bind /tmp/shiny-server.ie3djR/lib:/var/lib/shiny-server \
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--bind shiny-server.conf:/etc/shiny-server/shiny-server.conf <CONTAINER>
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---------------------------------------------------------------------------
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For custom applications, also add --bind /srv/shiny-server:/srv/shiny-server
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To see your applications, open your browser to http://127.0.0.1:15910 or
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open a ssh connection from your computer to your cluster.
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```
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2. Run the following command on your server
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```
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singularity run --bind /tmp/shiny-server.ie3djR/logs:/var/log/shiny \
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--bind /tmp/shiny-server.ie3djR/lib:/var/lib/shiny-server \
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--bind shiny-server.conf:/etc/shiny-server/shiny-server.conf docker://jd21/methylr:latest
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```
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3. The terminal will prompt likes
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```
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INFO: Using cached SIF image
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INFO: Converting SIF file to temporary sandbox...
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[2023-07-31T06:44:52.258] [INFO] shiny-server - Shiny Server v1.5.18.979 (Node.js v12.22.6)
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[2023-07-31T06:44:52.259] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
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[2023-07-31T06:44:52.285] [INFO] shiny-server - Starting listener on http://[::]:15910
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```
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<Control>+click or run `localhost:15910` on the browser.
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#### MacOS (Intel) and Windows AMD64 OS architecture
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**Please follow the [manual](https://methylr.netlify.app/dockercontainer.html)**.

‎prepare_template.sh

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#!/bin/bash
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# Thanks to https://github.com/vsoch/singularity-shiny
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usage () {
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echo "Steps:
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----------------------------------------------------------------------
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1. Use this script to prepare your shiny-server.conf (configuration)
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/bin/bash prepare_template.sh
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----------------------------------------------------------------------
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2. If needed, you can provide the following arguments
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Commands:
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help: show help and exit
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start: the generation of your config
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Options:
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--port: the port for the application (e.g., shiny default is 3737)
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--user: the user for the run_as directive in the shiny configuration
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--base: base folder with applications
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--logs: temporary folder with write for logs (not required)
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--disable-index: disable directory indexing
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----------------------------------------------------------------------
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3. Make sure Singularity is loaded, and run the container using
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the commands shown by the template.
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"
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}
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# Start the application
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SHINY_START="no";
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# Port for Flask
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CHECK_PORT="notnull"
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while [[ ! -z $CHECK_PORT ]]; do
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SHINY_PORT=$(( ( RANDOM % 60000 ) + 1025 ))
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CHECK_PORT=$(netstat -atn | grep $SHINY_PORT)
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done
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# Base for apps
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SHINY_BASE=/srv/shiny-server;
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# Log folder assumed to be bound to
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SHINY_LOGS=$(mktemp -d /tmp/shiny-server.XXXXXX) && rmdir ${SHINY_LOGS};
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# Disable indexing (on, default, is not disabled)
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DISABLE_DIRINDEX="on";
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# User to run_as, defaults to docker
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SHINY_USER="${USER}"
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if [ $# -eq 0 ]; then
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usage
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exit
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fi
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while true; do
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case ${1:-} in
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-h|--help|help)
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usage
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exit
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;;
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-s|--start|start)
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SHINY_START="yes"
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shift
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;;
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-p|--port|port)
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shift
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SHINY_PORT="${1:-}"
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shift
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;;
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-b|--base|base)
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shift
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SHINY_BASE="${1:-}"
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shift
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;;
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-u|--user)
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shift
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SHINY_USER="${1:-}"
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shift
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;;
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-di|--disable-index|disable-index)
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DISABLE_DIRINDEX="off"
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shift
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;;
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-l|logs|--logs)
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shift
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SHINY_LOGS="${1:-}"
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shift
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;;
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-*)
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echo "Unknown option: ${1:-}"
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exit 1
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;;
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*)
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break
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;;
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esac
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done
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# Functions
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function prepare_conf() {
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SHINY_PORT=$1
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SHINY_BASE=$2
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SHINY_LOGS=$3
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DISABLE_DIRINDEX=$4
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SHINY_USER=$5
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CONFIG="run_as ${SHINY_USER};
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server {
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listen ${SHINY_PORT};
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# Define a location at the base URL
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location / {
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# Host the directory of Shiny Apps stored in this directory
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site_dir ${SHINY_BASE};
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# Log all Shiny output to files in this directory
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log_dir ${SHINY_LOGS};
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# When a user visits the base URL rather than a particular application,
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# an index of the applications available in this directory will be shown.
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directory_index ${DISABLE_DIRINDEX};
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}
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}"
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echo "${CONFIG}";
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}
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# Are we starting the server?
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if [ "${SHINY_START}" == "yes" ]; then
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echo "Generating shiny configuration...";
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echo "port: ${SHINY_PORT}";
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echo "logs:" ${SHINY_LOGS};
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echo "base: ${SHINY_BASE}";
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echo "run_as: ${SHINY_USER}";
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# Prepare the template
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CONFIG=$(prepare_conf $SHINY_PORT $SHINY_BASE $SHINY_LOGS $DISABLE_DIRINDEX $SHINY_USER);
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# Temporary directories, if don't exist
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mkdir -p "${SHINY_LOGS}";
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mkdir -p ${SHINY_LOGS}/logs;
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mkdir -p ${SHINY_LOGS}/lib;
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# Configuration file
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echo "${CONFIG}" > "shiny-server.conf";
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echo "Server logging will be in ${SHINY_LOGS}";
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echo
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echo "To run your server:
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module load singularity
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singularity run --bind $SHINY_LOGS/logs:/var/log/shiny \\
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--bind $SHINY_LOGS/lib:/var/lib/shiny-server \\
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--bind shiny-server.conf:/etc/shiny-server/shiny-server.conf shiny.simg
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---------------------------------------------------------------------------
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For custom applications, also add --bind $SHINY_BASE:/srv/shiny-server
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To see your applications, open your browser to http://127.0.0.1:$SHINY_PORT or
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open a ssh connection from your computer to your cluster.
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"
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exit
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else
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usage
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fi

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