Explicitly include PyPI as an --extra-index-url to pip so we can install

from PyPI even when a package exists (but the correct version or
architecture does not exist) on wheels.galaxyproject.org. Previously,
PyPI was only checked after wheels.galaxyproject.org because pypiserver
performs an automatic redirect to PyPI for any packages that do not
exist in its index.

scripts/common_startup.sh

@@ -139,9 +139,9 @@ if [ $REPLACE_PIP -eq 1 ]; then
 fi
 
 if [ $FETCH_WHEELS -eq 1 ]; then
-    pip install -r requirements.txt --index-url "${GALAXY_WHEELS_INDEX_URL}"
+    pip install -r requirements.txt --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url https://pypi.python.org/pypi
     GALAXY_CONDITIONAL_DEPENDENCIES=$(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}"
+    [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url https://pypi.python.org/pypi
 fi
 
 if [ $FETCH_WHEELS -eq 1 -a $DEV_WHEELS -eq 1 ]; then