run_galaxy.sh

#!/bin/sh

#This script should be run from inside the Galaxy base directory

# If there is a file that defines a shell environment specific to this
# instance of Galaxy, source the file.
if [ -z "$GALAXY_LOCAL_ENV_FILE" ];
then
    GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
fi

if [ -f $GALAXY_LOCAL_ENV_FILE ];
then
    . $GALAXY_LOCAL_ENV_FILE
fi

./scripts/common_startup.sh || exit 1

# If there is a .venv/ directory, assume it contains a virtualenv that we
# should run this instance in.
if [ -d .venv ];
then
    echo "Activating virtualenv at %s/.venv\n" "$(pwd)"
    . .venv/bin/activate
fi

python ./scripts/check_python.py || exit 1

if [ -z "$GALAXY_CONFIG_FILE" ]; then
    if [ -f universe_wsgi.ini ]; then
        GALAXY_CONFIG_FILE=universe_wsgi.ini
    elif [ -f config/galaxy.ini ]; then
        GALAXY_CONFIG_FILE=config/galaxy.ini
    else
        GALAXY_CONFIG_FILE=config/galaxy.ini.sample
    fi
    export GALAXY_CONFIG_FILE
fi

if [ -n "$GALAXY_RUN_ALL" ]; then
    servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
    if ! echo "$@" | grep -q 'daemon\|restart'; then
        echo "ERROR: \$GALAXY_RUN_ALL cannot be used without the '--daemon', '--stop-daemon', 'restart', 'start' or 'stop' arguments to run.sh"
        exit 1
    fi
    (echo "$@" | grep -q -e '--daemon\|restart') && (echo "$@" | grep -q -e '--wait')
    WAIT=$?
    ARGS=$(echo "$@" | sed 's/--wait//')
    for server in $servers; do
        if [ $WAIT -eq 0 ]; then
            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $ARGS
            while true; do
                sleep 1
                # Grab the current pid from the pid file and remove any trailing space
                if ! current_pid_in_file=$(sed -e 's/[[:space:]]*$//' "$server.pid"); then
                    echo "A Galaxy process died, interrupting" >&2
                    exit 1
                fi
                if [ -n "$current_pid_in_file" ]; then
                    echo "Found PID $current_pid_in_file in '$server.pid', monitoring '$server.log'"
                else
                    echo "No PID found in '$server.pid' yet"
                    continue
                fi
                # Search for all pids in the logs and tail for the last one
                latest_pid=$(grep '^Starting server in PID [0-9]\+\.$' "$server.log" | sed 's/^Starting server in PID \([0-9]\{1,\}\).$/\1/' | tail -n 1)
                # If they're equivalent, then the current pid file agrees with our logs
                # and we've succesfully started
                [ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
            done
            echo
        else
            echo "Handling $server with log file $server.log..."
            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $@
        fi
    done
else
    # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main")
    python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" $@
fi