Make Galaxy installable the Pythonic way via setup.py. Incomplete, but

if you install it and then run `galaxy` from the root of a Galaxy clone,
after installing all the dependencies (see the end of
./scripts/common_startup.sh), it should start.

scripts/galaxy

@@ -0,0 +1,126 @@
+#!/bin/bash
+
+show_help() {
+cat <<EOF
+Usage:
+
+${0##*/} --daemon
+    Start Galaxy server as daemon process (paster):
+${0##*/} --stop-daemon
+    Stop Galaxy daemon process (paster)
+
+Extra Options:
+
+  -m|--mode   How to launch (paster,uwsgi,webless).
+              In webless mode Galaxy will not attempt to bind to a port,
+              this may be useful for Galaxy server processes acting as job
+              handlers.
+  -c|--config Configuration directory for Galaxy, defaults to ./config
+              Can also set with GALAXY_CONFIG_DIR environment variable.
+
+EOF
+}
+
+MODE=""
+while :
+do
+    case "$1" in
+      -h|--help|-\?) 
+          show_help
+          exit 0
+          ;;
+      -m|--mode)
+          if [ $# -gt 1 ]; then
+              MODE=$2
+              shift 2
+          else 
+              echo "--mode requires explicit argument" 1>&2
+              exit 1
+          fi          
+          ;;
+      -c|--config)
+          if [ $# -gt 1 ]; then
+              GALAXY_CONFIG_DIR=$2
+              shift 2
+          else 
+              echo "--config requires explicit argument" 1>&2
+              exit 1
+          fi
+          ;;
+      --) 
+          shift
+          break
+          ;;
+      *)
+          break;
+          ;;
+    esac
+done
+
+SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+PROJECT_DIRECTORY=$SCRIPTS_DIRECTORY/..
+
+GALAXY_CONFIG_DIR=${GALAXY_CONFIG_DIR:-"./config"}
+export GALAXY_CONFIG_DIR
+
+GALAXY_LOCAL_ENV=${GALAXY_LOCAL_ENV:-$GALAXY_CONFIG_DIR/local_env.sh}
+export GALAXY_LOCAL_ENV
+
+GALAXY_VIRTUALENV=${GALAXY_VIRTUALENV:-$PROJECT_DIRECTORY/.venv}
+export GALAXY_VIRTUALENV
+
+if [ -e $GALAXY_LOCAL_ENV ];
+then
+    echo "Sourcing file $GALAXY_LOCAL_ENV"
+    . $GALAXY_LOCAL_ENV
+fi
+
+if [ -d $GALAXY_VIRTUALENV ]; 
+then
+    echo "Activating virtual environment $GALAXY_VIRTUALENV/bin/activate"
+    . $GALAXY_VIRTUALENV/bin/activate
+fi
+
+GALAXY_CONFIG_SAMPLE_FILE="${PROJECT_DIRECTORY}/galaxy.ini.sample"
+if [ -z "$GALAXY_CONFIG_FILE" ]; then
+    if [ -f "${GALAXY_CONFIG_DIR}/galaxy.ini" ]; then
+        GALAXY_CONFIG_FILE="${GALAXY_CONFIG_DIR}/galaxy.ini"
+    else
+        GALAXY_CONFIG_FILE="$GALAXY_CONFIG_SAMPLE_FILE"
+    fi
+    export GALAXY_CONFIG_FILE
+fi
+
+if [ -z "$MODE" ]; 
+then
+    if hash uwsgi 2>/dev/null; then
+        MODE="uwsgi"
+    else
+        MODE="paster"
+    fi
+fi
+
+if [ "$MODE" == "uwsgi" ]; then
+    echo "Starting galaxy with command [uwsgi --ini-paste \"$GALAXY_CONFIG_FILE\" \"$@\"]"
+    uwsgi --ini-paste "$GALAXY_CONFIG_FILE" "$@"
+elif [ "$MODE" == "paster" ]; then
+    echo "Starting galaxy with command [galaxy-paster serve \"$GALAXY_CONFIG_FILE\" \"$@\"]"
+    galaxy-paster serve "$GALAXY_CONFIG_FILE" "$@"
+elif [ "$MODE" == "webless" ]; then
+    if hash galaxy-main 2>/dev/null; then
+        # Running from pip install since
+        # galaxy-main is available on PATH.
+        echo "Starting galaxy with command [galaxy-main]"
+        galaxy-main
+    else
+        # Running locally.
+        PROJECT_DIRECTORY=$GALAXY_SCRIPTS_DIR/..
+        cd $PROJECT_DIRECTORY
+        export PYTHONPATH=.:$PYTHONPATH
+        echo "Starting galaxy with command [python lib/galaxy/main.py]"
+        python lib/pulsar/main.py
+    fi
+else
+    echo "Unknown mode passed to --mode argument." 1>&2
+    exit 1
+fi