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#3 to fix Singularity container run, we added a bash script and 'how to run' details on README.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| #!/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: | ||
| ---------------------------------------------------------------------- | ||
| 1. Use this script to prepare your shiny-server.conf (configuration) | ||
| /bin/bash prepare_template.sh | ||
| ---------------------------------------------------------------------- | ||
| 2. If needed, you can provide the following arguments | ||
| Commands: | ||
| help: show help and exit | ||
| start: the generation of your config | ||
| Options: | ||
| --port: the port for the application (e.g., shiny default is 3737) | ||
| --user: the user for the run_as directive in the shiny configuration | ||
| --base: base folder with applications | ||
| --logs: temporary folder with write for logs (not required) | ||
| --disable-index: disable directory indexing | ||
| ---------------------------------------------------------------------- | ||
| 3. Make sure Singularity is loaded, and run the container using | ||
| the commands shown by the template. | ||
| " | ||
| } | ||
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| # Start the application | ||
| SHINY_START="no"; | ||
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| # Port for Flask | ||
| CHECK_PORT="notnull" | ||
| while [[ ! -z $CHECK_PORT ]]; do | ||
| SHINY_PORT=$(( ( RANDOM % 60000 ) + 1025 )) | ||
| CHECK_PORT=$(netstat -atn | grep $SHINY_PORT) | ||
| done | ||
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| # Base for apps | ||
| SHINY_BASE=/srv/shiny-server; | ||
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| # Log folder assumed to be bound to | ||
| SHINY_LOGS=$(mktemp -d /tmp/shiny-server.XXXXXX) && rmdir ${SHINY_LOGS}; | ||
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| # Disable indexing (on, default, is not disabled) | ||
| DISABLE_DIRINDEX="on"; | ||
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| # User to run_as, defaults to docker | ||
| SHINY_USER="${USER}" | ||
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| if [ $# -eq 0 ]; then | ||
| usage | ||
| exit | ||
| fi | ||
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| while true; do | ||
| case ${1:-} in | ||
| -h|--help|help) | ||
| usage | ||
| exit | ||
| ;; | ||
| -s|--start|start) | ||
| SHINY_START="yes" | ||
| shift | ||
| ;; | ||
| -p|--port|port) | ||
| shift | ||
| SHINY_PORT="${1:-}" | ||
| shift | ||
| ;; | ||
| -b|--base|base) | ||
| shift | ||
| SHINY_BASE="${1:-}" | ||
| shift | ||
| ;; | ||
| -u|--user) | ||
| shift | ||
| SHINY_USER="${1:-}" | ||
| shift | ||
| ;; | ||
| -di|--disable-index|disable-index) | ||
| DISABLE_DIRINDEX="off" | ||
| shift | ||
| ;; | ||
| -l|logs|--logs) | ||
| shift | ||
| SHINY_LOGS="${1:-}" | ||
| shift | ||
| ;; | ||
| -*) | ||
| echo "Unknown option: ${1:-}" | ||
| exit 1 | ||
| ;; | ||
| *) | ||
| break | ||
| ;; | ||
| esac | ||
| done | ||
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| # Functions | ||
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| function prepare_conf() { | ||
| SHINY_PORT=$1 | ||
| SHINY_BASE=$2 | ||
| SHINY_LOGS=$3 | ||
| DISABLE_DIRINDEX=$4 | ||
| SHINY_USER=$5 | ||
| CONFIG="run_as ${SHINY_USER}; | ||
| server { | ||
| listen ${SHINY_PORT}; | ||
| # Define a location at the base URL | ||
| location / { | ||
| # Host the directory of Shiny Apps stored in this directory | ||
| site_dir ${SHINY_BASE}; | ||
| # Log all Shiny output to files in this directory | ||
| log_dir ${SHINY_LOGS}; | ||
| # When a user visits the base URL rather than a particular application, | ||
| # an index of the applications available in this directory will be shown. | ||
| directory_index ${DISABLE_DIRINDEX}; | ||
| } | ||
| }" | ||
| echo "${CONFIG}"; | ||
| } | ||
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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..."; | ||
| echo "port: ${SHINY_PORT}"; | ||
| echo "logs:" ${SHINY_LOGS}; | ||
| echo "base: ${SHINY_BASE}"; | ||
| 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 $SHINY_USER); | ||
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| # Temporary directories, if don't exist | ||
| mkdir -p "${SHINY_LOGS}"; | ||
| mkdir -p ${SHINY_LOGS}/logs; | ||
| mkdir -p ${SHINY_LOGS}/lib; | ||
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| # Configuration file | ||
| echo "${CONFIG}" > "shiny-server.conf"; | ||
| echo "Server logging will be in ${SHINY_LOGS}"; | ||
| echo | ||
| echo "To run your server: | ||
| module load singularity | ||
| singularity run --bind $SHINY_LOGS/logs:/var/log/shiny \\ | ||
| --bind $SHINY_LOGS/lib:/var/lib/shiny-server \\ | ||
| --bind shiny-server.conf:/etc/shiny-server/shiny-server.conf shiny.simg | ||
| --------------------------------------------------------------------------- | ||
| For custom applications, also add --bind $SHINY_BASE:/srv/shiny-server | ||
| To see your applications, open your browser to http://127.0.0.1:$SHINY_PORT or | ||
| open a ssh connection from your computer to your cluster. | ||
| " | ||
| exit | ||
| else | ||
| usage | ||
| fi |