add hack

galaxy/run.sh

@@ -0,0 +1,98 @@
+#!/bin/sh
+
+
+# Usage: ./run.sh <start|stop|restart>
+#
+#
+# Description: This script can be used to start or stop the galaxy
+# web application.
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+
+# If there is a file that defines a shell environment specific to this
+# instance of Galaxy, source the file.
+if [ -z "$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
+
+GALAXY_PID=${GALAXY_PID:-galaxy.pid}
+GALAXY_LOG=${GALAXY_LOG:-galaxy.log}
+PID_FILE=$GALAXY_PID
+LOG_FILE=$GALAXY_LOG
+
+parse_common_args $@
+
+run_common_start_up
+
+setup_python
+
+
+if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
+then
+    export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="$(pwd)/test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
+    export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
+    export GALAXY_CONFIG_INTERACTIVETOOLS_ENABLE="true"
+    export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
+fi
+
+set_galaxy_config_file_var
+
+
+if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
+    # Install Conda environment if needed.
+    python ./scripts/manage_tool_dependencies.py init_if_needed
+fi
+
+[ -n "$GALAXY_UWSGI" ] && APP_WEBSERVER='uwsgi'
+find_server "${GALAXY_CONFIG_FILE:-none}" galaxy
+server_args=`echo $server_args | sed 's/--py-call-osafterfork//g'`
+
+
+if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
+    servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
+    if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; 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
+    for server in $servers; do
+        echo "Executing: python $server_args --server-name=\"$server\" --pid-file=\"$server.pid\" --log-file=\"$server.log\""
+        eval python $server_args --server-name="$server" --pid-file="$server.pid" --log-file="$server.log"
+        if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
+            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
+        fi
+    done
+else
+
+    echo "Executing: $run_server $server_args"
+    # args are properly quoted so use eval
+    eval $run_server $server_args
+fi