diff --git a/run.sh b/run.sh
index 8e821f238a3..8453587280e 100755
--- a/run.sh
+++ b/run.sh
@@ -18,7 +18,7 @@ fi
 while :
 do
     case "$1" in
-        --skip-eggs|--skip-wheels|--skip-samples|--dev-wheels|--no-create-venv|--no-replace-pip)
+        --skip-eggs|--skip-wheels|--skip-samples|--dev-wheels|--no-create-venv|--no-replace-pip|--replace-pip)
             common_startup_args="$common_startup_args $1"
             shift
             ;;
@@ -56,11 +56,12 @@ done
 
 # If there is a .venv/ directory, assume it contains a virtualenv that we
 # should run this instance in.
-if [ -d .venv -a -z "$skip_venv" ];
+GALAXY_VIRTUAL_ENV="${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 %s/.venv\n" $(pwd)
-    . .venv/bin/activate
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 # If you are using --skip-venv we assume you know what you are doing but warn
diff --git a/run_tests.sh b/run_tests.sh
index b91e618f010..c4cf50e493a 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -296,6 +296,10 @@ do
           no_replace_pip='--no-replace-pip'
           shift
           ;;
+      --replace-pip)
+          replace_pip='--replace-pip'
+          shift
+          ;;
       --skip-common-startup)
           # Don't run ./scripts/common_startup.sh (presumably it has already
           # been done, or you know what you're doing).
@@ -322,13 +326,14 @@ if [ -z "$skip_common_startup" ]; then
             GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=$GALAXY_TEST_DBURI
             export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
     fi
-    ./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip --dev-wheels || exit 1
+    ./scripts/common_startup.sh $skip_venv $no_create_venv $no_replace_pip $replace_pip --dev-wheels || exit 1
 fi
 
-if [ -z "$skip_venv" -a -d .venv ];
+GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
+if [ -z "$skip_venv" -a -d "$GALAXY_VIRTUAL_ENV" ];
 then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 if [ -n "$migrated_test" ] ; then
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index 98365595b31..bb5fd8243d1 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -1,19 +1,24 @@
 #!/bin/bash
 set -e
 
+SET_VENV=1
+for arg in "$@"; do
+    [ "$arg" = "--skip-venv" ] && SET_VENV=0
+done
+
 DEV_WHEELS=0
 FETCH_WHEELS=1
-SET_VENV=1
 CREATE_VENV=1
-REPLACE_PIP=1
+REPLACE_PIP=$SET_VENV
 COPY_SAMPLE_FILES=1
+
 for arg in "$@"; do
     [ "$arg" = "--skip-eggs" ] && FETCH_WHEELS=0
     [ "$arg" = "--skip-wheels" ] && FETCH_WHEELS=0
     [ "$arg" = "--dev-wheels" ] && DEV_WHEELS=1
-    [ "$arg" = "--skip-venv" ] && SET_VENV=0
     [ "$arg" = "--no-create-venv" ] && CREATE_VENV=0
     [ "$arg" = "--no-replace-pip" ] && REPLACE_PIP=0
+    [ "$arg" = "--replace-pip" ] && REPLACE_PIP=1
     [ "$arg" = "--stop-daemon" ] && FETCH_WHEELS=0
     [ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
 done
@@ -61,14 +66,16 @@ if [ ! -f $GALAXY_CONFIG_FILE ]; then
     GALAXY_CONFIG_FILE=config/galaxy.ini.sample
 fi
 
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
 if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
     # If .venv does not exist, attempt to create it.
-    if [ ! -d .venv ]
+    if [ ! -d "$GALAXY_VIRTUAL_ENV" ]
     then
         # Ensure Python is a supported version before creating .venv
         python ./scripts/check_python.py || exit 1
         if command -v virtualenv >/dev/null; then
-            virtualenv .venv
+            virtualenv "$GALAXY_VIRTUAL_ENV"
         else
             vvers=13.1.2
             vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
@@ -93,7 +100,7 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
                 python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
             fi
             tar zxf $vsrc -C $vtmp
-            python $vtmp/virtualenv-$vvers/virtualenv.py .venv
+            python $vtmp/virtualenv-$vvers/virtualenv.py "$GALAXY_VIRTUAL_ENV"
             rm -rf $vtmp
         fi
     fi
@@ -102,10 +109,10 @@ fi
 if [ $SET_VENV -eq 1 ]; then
     # If there is a .venv/ directory, assume it contains a virtualenv that we
     # should run this instance in.
-    if [ -d .venv ];
+    if [ -d "$GALAXY_VIRTUAL_ENV" ];
     then
-        printf "Activating virtualenv at %s/.venv\n" $(pwd)
-        . .venv/bin/activate
+        printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+        . "$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
         # problems when there are conflicts with Galaxy's dependencies outside
@@ -117,13 +124,13 @@ if [ $SET_VENV -eq 1 ]; then
     fi
 
     if [ -z "$VIRTUAL_ENV" ]; then
-        echo "ERROR: A virtualenv cannot be found. Please create a virtualenv in .venv, or activate one."
+        echo "ERROR: A virtualenv cannot be found. Please create a virtualenv in $GALAXY_VIRTUAL_ENV, or activate one."
         exit 1
     fi
 fi
 
 : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
-if [ $SET_VENV -eq 1 -a $REPLACE_PIP -eq 1 ]; then
+if [ $REPLACE_PIP -eq 1 ]; then
     pip_version=`pip --version | awk '{print $2}'`
     pre=`python -c "from pkg_resources import parse_version; from sys import stdout; stdout.write('--pre') if parse_version('$pip_version') >= parse_version('1.4') else stdout.write('')"`
     pip install $pre --no-index --find-links ${GALAXY_WHEELS_INDEX_URL}/pip --upgrade pip