diff --git a/run.sh b/run.sh
index 901d7e46172..039047a87b8 100755
--- a/run.sh
+++ b/run.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 # If there is a file that defines a shell environment specific to this
 # instance of Galaxy, source the file.
@@ -34,7 +34,7 @@ do
             shift
             ;;
         --daemon|--restart|restart)
-            if [ "$1"=="--restart" ]
+            if [ "$1" = "--restart" ]
             then
                 paster_args="$paster_args restart"
             else
@@ -66,7 +66,7 @@ GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
 if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ];
 then
     [ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
-    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
@@ -99,35 +99,35 @@ if [ -z "$GALAXY_CONFIG_FILE" ]; then
 fi
 
 if [ -n "$GALAXY_RUN_ALL" ]; then
-    servers=`sed -n 's/^\[server:\(.*\)\]/\1/  p' $GALAXY_CONFIG_FILE | xargs echo`
+    servers=$(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` or `restart` arguments to run.sh'
+        echo "ERROR: \$GALAXY_RUN_ALL cannot be used without the '--daemon', '--stop-daemon' or 'restart' arguments to run.sh"
         exit 1
     fi
     for server in $servers; do
         if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
-            python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $paster_args
+            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
             while true; do
                 sleep 1
                 printf "."
                 # Grab the current pid from the pid file
-                if ! current_pid_in_file=$(cat $server.pid); then
+                if ! current_pid_in_file=$(cat "$server.pid"); then
                     echo "A Galaxy process died, interrupting" >&2
                     exit 1
                 fi
                 # Search for all pids in the logs and tail for the last one
-                latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1`
+                latest_pid=$(egrep '^Starting server in PID [0-9]+\.$' "$server.log" -o | sed 's/Starting server in PID //g;s/\.$//g' | 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 $current_pid_in_file ] && break
+                [ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
             done
             echo
         else
             echo "Handling $server with log file $server.log..."
-            python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $paster_args
+            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
         fi
     done
 else
     # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main")
-    python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $paster_args
+    python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" $paster_args
 fi
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index fbf4180d22e..c7c1d1758d0 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 set -e
 
 SET_VENV=1
@@ -54,22 +54,22 @@ if [ $COPY_SAMPLE_FILES -eq 1 ]; then
 	for sample in $SAMPLES; do
 		file=${sample%.sample}
 	    if [ ! -f "$file" -a -f "$sample" ]; then
-	        echo "Initializing $file from `basename $sample`"
-	        cp $sample $file
+	        echo "Initializing $file from $(basename "$sample")"
+	        cp "$sample" "$file"
 	    fi
 	done
 fi
 
 # remove problematic cached files
 for rmfile in $RMFILES; do
-    [ -f $rmfile ] && rm -f $rmfile
+    [ -f "$rmfile" ] && rm -f "$rmfile"
 done
 
 : ${GALAXY_CONFIG_FILE:=config/galaxy.ini}
-if [ ! -f $GALAXY_CONFIG_FILE ]; then
+if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
     GALAXY_CONFIG_FILE=universe_wsgi.ini
 fi
-if [ ! -f $GALAXY_CONFIG_FILE ]; then
+if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
     GALAXY_CONFIG_FILE=config/galaxy.ini.sample
 fi
 
@@ -87,24 +87,24 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
             vvers=13.1.2
             vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
             vsha="aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc"
-            vtmp=`mktemp -d -t galaxy-virtualenv-XXXXXX`
-            vsrc="$vtmp/`basename $vurl`"
+            vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
+            vsrc="$vtmp/$(basename $vurl)"
             # SSL certificates are not checked to prevent problems with messed
             # up client cert environments. We verify the download using a known
             # good sha256 sum instead.
             echo "Fetching $vurl"
             if command -v curl >/dev/null; then
-                curl --insecure -L -o $vsrc $vurl
+                curl --insecure -L -o "$vsrc" "$vurl"
             elif command -v wget >/dev/null; then
-                wget --no-check-certificate -O $vsrc $vurl
+                wget --no-check-certificate -O "$vsrc" "$vurl"
             else
                 python -c "import urllib; urllib.urlretrieve('$vurl', '$vsrc')"
             fi
             echo "Verifying $vsrc checksum is $vsha"
             python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
-            tar zxf $vsrc -C $vtmp
-            python $vtmp/virtualenv-$vvers/virtualenv.py "$GALAXY_VIRTUAL_ENV"
-            rm -rf $vtmp
+            tar zxf "$vsrc" -C "$vtmp"
+            python "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
+            rm -rf "$vtmp"
         fi
     fi
 fi
@@ -114,7 +114,7 @@ if [ $SET_VENV -eq 1 ]; then
     # should run this instance in.
     if [ -d "$GALAXY_VIRTUAL_ENV" ];
     then
-        printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+        echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
         . "$GALAXY_VIRTUAL_ENV/bin/activate"
         # Because it's a virtualenv, we assume $PYTHONPATH is unnecessary for
         # anything in the venv to work correctly, and having it set can cause
@@ -131,7 +131,7 @@ if [ $SET_VENV -eq 1 ]; then
         exit 1
     fi
 elif [ $SET_VENV -eq 0 -a $CONDA_ALREADY_INSTALLED -eq 1 ]; then
-    echo -e "\e[33mWarning: You have Conda installed. Skipping virtualenv activation. This could cause missing dependencies.\e[0m"
+    echo "Warning: You have Conda installed. Skipping virtualenv activation. This could cause missing dependencies."
 fi
 
 : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
@@ -140,12 +140,12 @@ if [ $REPLACE_PIP -eq 1 ]; then
 fi
 
 if [ $FETCH_WHEELS -eq 1 ]; then
-    pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL}
-    GALAXY_CONDITIONAL_DEPENDENCIES=`PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))"`
-    [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url ${GALAXY_WHEELS_INDEX_URL}
+    pip install -r requirements.txt --index-url "${GALAXY_WHEELS_INDEX_URL}"
+    GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))")
+    [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}"
 fi
 
 if [ $FETCH_WHEELS -eq 1 -a $DEV_WHEELS -eq 1 ]; then
     dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
-    [ -f $dev_requirements ] && pip install -r $dev_requirements --index-url ${GALAXY_WHEELS_INDEX_URL}
+    [ -f $dev_requirements ] && pip install -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}"
 fi