galaxy init scripts

galaxy-base

#!/bin/bash

# Author: Renato Alves, 2013

function usage {
    echo "WARNING: $0 should not be used directly"
    echo " Create a symlink to $0 with a name in the format 'galaxy-NAME'"
    echo " NAME should be 'toolshed' or anything matching [server:NAME] in your config/galaxy.ini"
    echo "E.g. galaxy-web0 , galaxy-job0 or galaxy-toolshed"
    exit 1
}

# Will hold the final part of current script name "galaxy-(SERVER)"
if [[ "${0}" == *galaxy-* ]]; then
    SERVER=${0##*-}
    if [ $SERVER == "base" ]; then
        usage
    fi
else
    usage
fi

### BEGIN INIT INFO
# Provides:             galaxy-$SERVER
# Required-Start:       $network $local_fs
# Required-Stop:
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    Galaxy $SERVER
### END INIT INFO

HOME=/home/Users/galaxy/galaxy_files
VENV="$HOME/galaxy_env"
DIR="$HOME/galaxy_dist"

PATH=$VENV/bin/:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
USER=galaxy
GROUP=galaxy
DAEMON=/bin/sh

NAME=galaxy-$SERVER

LOGFILE=/var/log/$USER/$NAME.log
PIDFILE=/var/run/$USER/$NAME.pid

if [ "$NAME" == "galaxy-toolshed" ]; then
    DAEMON_OPTS="$DIR/run_tool_shed.sh --log-file=$LOGFILE --pid-file=$PIDFILE"
else
    DAEMON_OPTS="$DIR/run.sh --log-file=$LOGFILE --server-name=$SERVER --pid-file=$PIDFILE"
fi

# Removed exit on error as this causes premature aborts and makes it impossible
# to use commands that are expected to fail
#set -e

. /lib/lsb/init-functions

case "$1" in
    start)
        log_daemon_msg "Starting Galaxy" "$SERVER"
        LOGFOLDER="$(dirname $LOGFILE)"
        PIDFOLDER="$(dirname $PIDFILE)"

        # Make sure log and run folders exist and are owned by $USER before launch
        # but only if LOGFOLDER and PIDFOLDER end with $USER
        if [[ "$(basename $LOGFOLDER)" == "$USER" && "$(basename $PIDFOLDER)" == "$USER" ]]; then
            if ! [ -d "$LOGFOLDER" ]; then
                mkdir "$LOGFOLDER"
            fi
            chown $USER.$GROUP $LOGFOLDER

            if ! [ -d "$PIDFOLDER" ]; then
                mkdir "$PIDFOLDER"
            fi
            chown $USER.$GROUP $PIDFOLDER
        fi

        start-stop-daemon --chuid $USER --group $GROUP --start \
            --pidfile $PIDFILE --exec $DAEMON -- $DAEMON_OPTS --daemon > /dev/null
        log_end_msg $?
        ;;

    stop)
        log_daemon_msg "Stopping Galaxy" "$SERVER"
        start-stop-daemon --stop --pidfile $PIDFILE -- --stop-daemon
        log_end_msg $?
        ;;

    restart|force-reload)
        # restart commands here
        $0 stop
        sleep 1
        $0 start
        ;;

    status)
        status_of_proc -p $PIDFILE $DAEMON $NAME && exit 0 || exit $?
        ;;

    *)
        echo "Usage: $0 start|stop|restart|force-reload|status"
        exit 1
        ;;
esac

galaxy-init

#!/bin/bash

# Author: Renato Alves, 2014

### BEGIN INIT INFO
# Provides:             galaxy-init
# Required-Start:       $network $local_fs
# Required-Stop:
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    Initialize all galaxy components
### END INIT INFO

PATH=$VENV/bin/:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

#set -e

function get_components {
    for g in ${DIR}/galaxy-*; do
        # Do nothing for galaxy-init and galaxy-base
        case "$g" in
            ${DIR}/galaxy-init|${DIR}/galaxy-base)
                continue
                ;;
            *)
                echo $g
        esac
    done
}

function check_status {
    # Check the status of the current galaxy component in a subshell
    if [ "$2" == "verbose" ]; then
        ($1 status)
    else
        ($1 status) > /dev/null
        echo $?
    fi
}

function check_status_verbose {
    check_status $1 "verbose"
}

. /lib/lsb/init-functions

case "$1" in
    start)
        for g in $(get_components); do
            # Check the status of the current galaxy component in a subshell
            STATUS=$(check_status $g)
            if [ "$STATUS" != "0" ]; then
                $g start
            else
                SERVER="galaxy-${g##*-}"
                echo "Not starting $SERVER - already running"
            fi
        done
        ;;

    stop)
        for g in $(get_components); do
            # Check the status of the current galaxy component in a subshell
            STATUS=$(check_status $g)
            if [ "$STATUS" == "0" ]; then
                $g stop
            else
                SERVER="galaxy-${g##*-}"
                echo "Not stopping $SERVER - already stopped with status $STATUS"
            fi
        done
        ;;

    restart|force-reload)
        # restart commands here
        $0 stop
        sleep 1
        $0 start
        ;;

    status)
        for g in $(get_components); do
            check_status_verbose $g
        done
        ;;

    *)
        echo "Usage: $0 start|stop|restart|force-reload|status"
        exit 1
        ;;
esac