diff --git a/polaris/config.py b/polaris/config.py
index 49ad726d9..868a9bea4 100644
--- a/polaris/config.py
+++ b/polaris/config.py
@@ -71,5 +71,8 @@ def _ensure_absolute_paths(self):
             if not config.has_section(section):
                 continue
             for option, value in config.items(section):
-                value = os.path.abspath(value)
-                config.set(section, option, value)
+                # not safe to make paths that start with other config options
+                # into absolute paths
+                if not value.startswith('$'):
+                    value = os.path.abspath(value)
+                    config.set(section, option, value)