Add generalization of install_tools_wrapper.sh

galaxy/Dockerfile

@@ -235,6 +235,8 @@ ADD ./tool_sheds_conf.xml $GALAXY_HOME/tool_sheds_conf.xml
 
 # Script that enables easier downstream installation of tools (e.g. for different Galaxy Docker flavours)
 ADD install_tools_wrapper.sh /usr/bin/install-tools
+ADD with-galaxy.sh /usr/bin/with-galaxy
+
 # script to install BioJS visualizations
 ADD install_biojs_vis.sh /usr/bin/install-biojs
 RUN chmod +x /usr/bin/install-tools /usr/bin/install-biojs && \

galaxy/with-galaxy.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# Enable Test Tool Shed
+export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml
+
+if pgrep "supervisord" > /dev/null
+then
+    echo "System is up and running. Starting with the installation."
+    export PORT=80
+else
+    # start Galaxy
+    export PORT=8080
+    service postgresql start
+    install_log='galaxy_install.log'
+
+    # wait for database to finish starting up
+    STATUS=$(psql 2>&1)
+    while [[ ${STATUS} =~ "starting up" ]]
+    do
+      echo "waiting for database: $STATUS"
+      STATUS=$(psql 2>&1)
+      sleep 1
+    done
+
+    echo "starting Galaxy"
+    sudo -E -u galaxy unset $SUDO_UID; ./run.sh -d $install_log --pidfile galaxy_install.pid --http-timeout 3000
+
+    galaxy_install_pid=`cat galaxy_install.pid`
+    galaxy-wait -g http://localhost:$PORT -v --timeout 120
+fi
+
+exec "$@"
+
+exit_code=$?
+
+if [ $exit_code != 0 ] ; then
+    if [ "$2" == "-v" ] ; then
+        echo "Command failed, Galaxy server log:"
+        cat $install_log
+    fi
+    # exit $exit_code Galaxy should be shut down properly
+fi
+
+if ! pgrep "supervisord" > /dev/null
+then
+    # stop everything
+    sudo -E -u galaxy ./run.sh --stop --pidfile galaxy_install.pid
+    rm $install_log
+    service postgresql stop
+fi
+
+exit $exit_code