mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 05:45:37 +08:00
John Chilton
6a7cc34e1b
- They now uniformly handle server option processing. - Reports and Tool Shed now respect many new and important options such as --skip_venv. - Reports and Tool Shed now do extra checking around Python version that Galaxy does. In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
88 lines
3.2 KiB
Bash
Executable File
88 lines
3.2 KiB
Bash
Executable File
#!/bin/sh
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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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./scripts/common_startup.sh $common_startup_args || exit 1
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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_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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if [ -z "$GALAXY_CONFIG_FILE" ]; then
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if [ -f universe_wsgi.ini ]; then
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GALAXY_CONFIG_FILE=universe_wsgi.ini
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elif [ -f config/galaxy.ini ]; then
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GALAXY_CONFIG_FILE=config/galaxy.ini
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else
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GALAXY_CONFIG_FILE=config/galaxy.ini.sample
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fi
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export GALAXY_CONFIG_FILE
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fi
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if [ $INITIALIZE_TOOL_DEPENDENCIES -eq 1 ]; then
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# Install Conda environment if needed.
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python ./scripts/manage_tool_dependencies.py -c "$GALAXY_CONFIG_FILE" init_if_needed
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fi
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if [ -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' or 'restart' arguments to run.sh"
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exit 1
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fi
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for server in $servers; do
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if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
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python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
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while true; do
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sleep 1
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printf "."
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# Grab the current pid from the pid file
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if ! current_pid_in_file=$(cat "$server.pid"); then
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echo "A Galaxy process died, interrupting" >&2
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exit 1
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fi
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# Search for all pids in the logs and tail for the last one
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latest_pid=$(egrep '^Starting server in PID [0-9]+\.$' "$server.log" -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1)
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# If they're equivalent, then the current pid file agrees with our logs
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# and we've succesfully started
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[ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
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done
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echo
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else
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echo "Handling $server with log file $server.log..."
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python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
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fi
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done
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else
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# Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main")
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python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" $paster_args
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fi
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