mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
Nicola Soranzo
97 lines
3.4 KiB
Bash
Executable File
97 lines
3.4 KiB
Bash
Executable File
#!/bin/sh
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# Usage: ./run.sh <start|stop|restart>
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#
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#
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# Description: This script can be used to start or stop the galaxy
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# web application.
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cd "$(dirname "$0")"
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. ./scripts/common_startup_functions.sh
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# If there is a file that defines a shell environment specific to this
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# instance of Galaxy, source the file.
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if [ -z "$GALAXY_LOCAL_ENV_FILE" ];
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then
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GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
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fi
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if [ -f "$GALAXY_LOCAL_ENV_FILE" ];
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then
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. "$GALAXY_LOCAL_ENV_FILE"
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fi
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GALAXY_PID=${GALAXY_PID:-galaxy.pid}
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GALAXY_LOG=${GALAXY_LOG:-galaxy.log}
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PID_FILE=$GALAXY_PID
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LOG_FILE=$GALAXY_LOG
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parse_common_args $@
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run_common_start_up
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setup_python
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if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
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then
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export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="test/functional/tools/samples_tool_conf.xml"
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export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
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export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_FORMAT="true"
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export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
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export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
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fi
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if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
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python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
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fi
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set_galaxy_config_file_var
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if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
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# Install Conda environment if needed.
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python ./scripts/manage_tool_dependencies.py init_if_needed
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fi
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[ -n "$GALAXY_UWSGI" ] && APP_WEBSERVER='uwsgi'
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find_server "${GALAXY_CONFIG_FILE:-none}" galaxy
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if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
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servers=$(sed -n 's/^\[server:\(.*\)\]/\1/ p' "$GALAXY_CONFIG_FILE" | xargs echo)
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if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; then
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echo "ERROR: \$GALAXY_RUN_ALL cannot be used without the '--daemon', '--stop-daemon', 'restart', 'start' or 'stop' arguments to run.sh"
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exit 1
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fi
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for server in $servers; do
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echo "Executing: python $server_args --server-name=\"$server\" --pid-file=\"$server.pid\" --log-file=\"$server.log\""
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eval python $server_args --server-name="$server" --pid-file="$server.pid" --log-file="$server.log"
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if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
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while true; do
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sleep 1
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# Grab the current pid from the pid file and remove any trailing space
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if ! current_pid_in_file=$(sed -e 's/[[:space:]]*$//' "$server.pid"); then
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echo "A Galaxy process died, interrupting" >&2
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exit 1
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fi
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if [ -n "$current_pid_in_file" ]; then
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echo "Found PID $current_pid_in_file in '$server.pid', monitoring '$server.log'"
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else
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echo "No PID found in '$server.pid' yet"
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continue
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fi
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# Search for all pids in the logs and tail for the last one
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latest_pid=$(grep '^Starting server in PID [0-9]\+\.$' "$server.log" | sed 's/^Starting server in PID \([0-9]\+\).$/\1/' | tail -n 1)
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# If they're equivalent, then the current pid file agrees with our logs
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# and we've succesfully started
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[ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
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done
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echo
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fi
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done
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else
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echo "Executing: $run_server $server_args"
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# args are properly quoted so use eval
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eval $run_server $server_args
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fi
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