diff --git a/run.sh b/run.sh
index 1ddbe3170b4..0210375afac 100755
--- a/run.sh
+++ b/run.sh
@@ -18,9 +18,9 @@ then
     GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
 fi
 
-if [ -f $GALAXY_LOCAL_ENV_FILE ];
+if [ -f "$GALAXY_LOCAL_ENV_FILE" ];
 then
-    . $GALAXY_LOCAL_ENV_FILE
+    . "$GALAXY_LOCAL_ENV_FILE"
 fi
 
 GALAXY_PID=${GALAXY_PID:-galaxy.pid}
@@ -46,30 +46,15 @@ if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
     python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
 fi
 
-if [ -z "$GALAXY_CONFIG_FILE" ]; then
-    if [ -f universe_wsgi.ini ]; then
-        GALAXY_CONFIG_FILE=universe_wsgi.ini
-    elif [ -f config/galaxy.ini ]; then
-        GALAXY_CONFIG_FILE=config/galaxy.ini
-    elif [ -f config/galaxy.yml ]; then
-        GALAXY_CONFIG_FILE=config/galaxy.yml
-    elif [ -f config/galaxy.ini.sample -a -z "$GALAXY_UWSGI" ]; then
-        GALAXY_CONFIG_FILE=config/galaxy.ini.sample
-    fi
-    export GALAXY_CONFIG_FILE
-fi
+set_galaxy_config_file_var
 
-if [ -n "$GALAXY_CONFIG_FILE" ]; then
-    config_file_arg="-c $GALAXY_CONFIG_FILE"
-fi
-
-if [ $INITIALIZE_TOOL_DEPENDENCIES -eq 1 ]; then
+if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
     # Install Conda environment if needed.
-    python ./scripts/manage_tool_dependencies.py $config_file_arg init_if_needed
+    python ./scripts/manage_tool_dependencies.py init_if_needed
 fi
 
 [ -n "$GALAXY_UWSGI" ] && APP_WEBSERVER='uwsgi'
-find_server ${GALAXY_CONFIG_FILE:-none} galaxy
+find_server "${GALAXY_CONFIG_FILE:-none}" galaxy
 
 if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
     servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
diff --git a/run_reports.sh b/run_reports.sh
index a8ab6b70b84..de869ad0e48 100755
--- a/run_reports.sh
+++ b/run_reports.sh
@@ -31,15 +31,7 @@ run_common_start_up
 setup_python
 
 if [ -z "$GALAXY_REPORTS_CONFIG" ]; then
-    if [ -f reports_wsgi.ini ]; then
-        GALAXY_REPORTS_CONFIG=reports_wsgi.ini
-    elif [ -f config/reports_wsgi.ini ]; then
-        GALAXY_REPORTS_CONFIG=config/reports_wsgi.ini
-    elif [ -f config/reports.ini ]; then
-        GALAXY_REPORTS_CONFIG=config/reports.ini
-    elif [ -f config/reports.yml ]; then
-        GALAXY_REPORTS_CONFIG=config/reports.yml
-    fi
+    GALAXY_REPORTS_CONFIG=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['reports', 'reports_wsgi']) or '')")
     export GALAXY_REPORTS_CONFIG
 fi
 
diff --git a/run_tool_shed.sh b/run_tool_shed.sh
index 171dc38ec58..06675f0a955 100755
--- a/run_tool_shed.sh
+++ b/run_tool_shed.sh
@@ -17,22 +17,16 @@ run_common_start_up
 setup_python
 
 
-tool_shed=`./scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh $parser_args`
+tool_shed=$(./scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh $parser_args)
 args=$parser_args
 
 if [ $? -eq 0 ] ; then
 	bash ./scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh $parser_args
-	args=`echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##"`
+	args=$(echo $@ | sed "s#-\?-bootstrap_from_tool_shed $tool_shed##")
 fi
 
 if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then
-    if [ -f tool_shed_wsgi.ini ]; then
-        TOOL_SHED_CONFIG_FILE=tool_shed_wsgi.ini
-    elif [ -f config/tool_shed.ini ]; then
-        TOOL_SHED_CONFIG_FILE=config/tool_shed.ini
-    elif [ -f config/tool_shed.yml ]; then
-        TOOL_SHED_CONFIG_FILE=config/tool_shed.yml
-    fi
+    TOOL_SHED_CONFIG_FILE=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['tool_shed', 'tool_shed_wsgi']) or '')")
     export TOOL_SHED_CONFIG_FILE
 fi
 
diff --git a/scripts/common_startup_functions.sh b/scripts/common_startup_functions.sh
index b1e9d18852a..fca6db04e75 100644
--- a/scripts/common_startup_functions.sh
+++ b/scripts/common_startup_functions.sh
@@ -87,9 +87,16 @@ setup_python() {
     python ./scripts/check_python.py || exit 1
 }
 
+set_galaxy_config_file_var() {
+    if [ -z "$GALAXY_CONFIG_FILE" ]; then
+        GALAXY_CONFIG_FILE=$(PYTHONPATH=lib python -c "from __future__ import print_function; from galaxy.util.properties import find_config_file; print(find_config_file(['galaxy', 'universe_wsgi']) or '')")
+        export GALAXY_CONFIG_FILE
+    fi
+}
+
 find_server() {
-    server_config="$1"
-    server_app="$2"
+    server_config=$1
+    server_app=$2
     arg_getter_args=
     default_webserver="paste"
     case "$server_config" in
@@ -110,17 +117,17 @@ find_server() {
             echo 'ERROR: Could not find uwsgi executable'
             exit 1
         fi
-        [ "$server_config" != "none" ] && arg_getter_args="-c $server_config"
+        [ "$server_config" != "none" ] && arg_getter_args="-c \"$server_config\""
         [ -n "$server_app" ] && arg_getter_args="--app $server_app"
         run_server="$UWSGI"
         server_args=
         if [ -z "$stop_daemon_arg_set" -a -z "$restart_arg_set" ]; then
-            server_args="$(python ./scripts/get_uwsgi_args.py $arg_getter_args)"
+            server_args="$(eval python ./scripts/get_uwsgi_args.py $arg_getter_args)"
         fi
         server_args="$server_args $uwsgi_args"
         pid_log_paster_args=""
     else
         run_server="python"
-        server_args="./scripts/paster.py serve $server_config $paster_args"
+        server_args="./scripts/paster.py serve \"$server_config\" $paster_args"
     fi
 }
diff --git a/scripts/common_startup_variables.sh b/scripts/common_startup_variables.sh
deleted file mode 100755
index dd3e9a95b1b..00000000000
--- a/scripts/common_startup_variables.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env bash
-
-# This file is sourced in the maintenance.sh script and could be sourced in ./run.sh or ./run_reports.sh
-SCRIPTLOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-# If there is a file that defines a shell environment specific to this
-# instance of Galaxy, source the file.
-if [ -z $GALAXY_LOCAL_ENV_FILE ];
-then
-  GALAXY_LOCAL_ENV_FILE="$SCRIPTLOCATION/../config/local_env.sh"
-fi
-
-if [ -f $GALAXY_LOCAL_ENV_FILE ];
-then
-  echo "Activating local env file: $GALAXY_LOCAL_ENV_FILE"
-  . $GALAXY_LOCAL_ENV_FILE
-fi
-
-# If there is a .venv/ directory, assume it contains a virtualenv that we
-# should run this instance in.
-GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-$SCRIPTLOCATION/../.venv}"
-if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ];
-then
-  [ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
-  echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
-  . "$GALAXY_VIRTUAL_ENV/bin/activate"
-fi
-if [ -z "$GALAXY_CONFIG_FILE" ]; then
-  if [ -f "$SCRIPTLOCATION/../universe_wsgi.ini" ]; then
-    GALAXY_CONFIG_FILE=universe_wsgi.ini
-  elif [ -f "$SCRIPTLOCATION/../config/galaxy.ini" ]; then
-    GALAXY_CONFIG_FILE=config/galaxy.ini
-  else
-    GALAXY_CONFIG_FILE=config/galaxy.ini.sample
-  fi
-  export GALAXY_CONFIG_FILE
-fi
-
-echo "GALAXY_CONFIG_FILE: ${GALAXY_CONFIG_FILE}"
diff --git a/scripts/maintenance.sh b/scripts/maintenance.sh
index 757da5efd00..8ca4771ed54 100755
--- a/scripts/maintenance.sh
+++ b/scripts/maintenance.sh
@@ -52,8 +52,13 @@ do
   esac
 done
 
-SCRIPTLOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-source ${SCRIPTLOCATION}/common_startup_variables.sh
+cd "$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"/../
+
+. scripts/common_startup_functions.sh
+
+setup_python
+
+set_galaxy_config_file_var
 
 if [ "$DRYRUN" = true ]; then
   MODE="--info_only"
@@ -61,14 +66,14 @@ else
   MODE="-r"
 fi
 
-MAINTENANCE_LOG="$SCRIPTLOCATION/../maintenance.log"
+MAINTENANCE_LOG=maintenance.log
 COMMANDS=(
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_userless_histories >> $MAINTENANCE_LOG"
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_histories >> $MAINTENANCE_LOG"
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG"
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_folders >> $MAINTENANCE_LOG"
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_datasets >> $MAINTENANCE_LOG"
-"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG")
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_userless_histories >> $MAINTENANCE_LOG"
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_histories >> $MAINTENANCE_LOG"
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG"
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_folders >> $MAINTENANCE_LOG"
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_datasets >> $MAINTENANCE_LOG"
+"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG")
 
 printf "\nDry run: $DRYRUN\nDays: $DAYS\n\n"
 echo "Will run following commands and output in $MAINTENANCE_LOG"
@@ -77,15 +82,14 @@ for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
 done
 
 if [ "$DRYRUN" = false ]; then
-  echo "python $SCRIPTLOCATION/set_user_disk_usage.py >> $MAINTENANCE_LOG"
+  echo "python scripts/set_user_disk_usage.py >> $MAINTENANCE_LOG"
 fi
 
 # Run the commands
-cd $SCRIPTLOCATION/../
 for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
   eval "${COMMANDS[$i]}"
 done
 
 if [ "$DRYRUN" = false ]; then
-  python $SCRIPTLOCATION/set_user_disk_usage.py >> $MAINTENANCE_LOG
+  python scripts/set_user_disk_usage.py >> $MAINTENANCE_LOG
 fi