diff --git a/dotbot/cli.py b/dotbot/cli.py
index 2680acf..77bd439 100644
--- a/dotbot/cli.py
+++ b/dotbot/cli.py
@@ -73,10 +73,10 @@ def main():
         if not isinstance(tasks, list):
             raise ReadingError('Configuration file must be a list of tasks')
         if options.base_directory:
-            base_directory = options.base_directory
+            base_directory = os.path.abspath(options.base_directory)
         else:
             # default to directory of config file
-            base_directory = os.path.dirname(os.path.realpath(options.config_file))
+            base_directory = os.path.dirname(os.path.abspath(options.config_file))
         os.chdir(base_directory)
         dispatcher = Dispatcher(base_directory)
         success = dispatcher.dispatch(tasks)
diff --git a/test/tests/link-canonicalize.bash b/test/tests/link-canonicalize.bash
new file mode 100644
index 0000000..34015c8
--- /dev/null
+++ b/test/tests/link-canonicalize.bash
@@ -0,0 +1,20 @@
+test_description='linking canonicalizes path by default'
+. '../test-lib.bash'
+
+test_expect_success 'setup' '
+echo "apple" > ${DOTFILES}/f &&
+ln -s dotfiles dotfiles-symlink
+'
+
+test_expect_success 'run' '
+cat > "${DOTFILES}/${INSTALL_CONF}" <<EOF
+- link:
+    ~/.f:
+      path: f
+EOF
+${DOTBOT_EXEC} -c dotfiles-symlink/${INSTALL_CONF}
+'
+
+test_expect_success 'test' '
+[ "$(readlink ~/.f | cut -d/ -f4-)" = "dotfiles/f" ]
+'
diff --git a/test/tests/link-no-canonicalize.bash b/test/tests/link-no-canonicalize.bash
new file mode 100644
index 0000000..f9ccb99
--- /dev/null
+++ b/test/tests/link-no-canonicalize.bash
@@ -0,0 +1,23 @@
+test_description='linking path canonicalization can be disabled'
+. '../test-lib.bash'
+
+test_expect_success 'setup' '
+echo "apple" > ${DOTFILES}/f &&
+ln -s dotfiles dotfiles-symlink
+'
+
+test_expect_success 'run' '
+cat > "${DOTFILES}/${INSTALL_CONF}" <<EOF
+- defaults:
+    link:
+      canonicalize-path: false
+- link:
+    ~/.f:
+      path: f
+EOF
+${DOTBOT_EXEC} -c ./dotfiles-symlink/${INSTALL_CONF}
+'
+
+test_expect_success 'test' '
+[ "$(readlink ~/.f | cut -d/ -f4-)" = "dotfiles-symlink/f" ]
+'