diff --git a/pre_commit/commands/install_uninstall.py b/pre_commit/commands/install_uninstall.py
index 6e09dabd..6d9d14d8 100644
--- a/pre_commit/commands/install_uninstall.py
+++ b/pre_commit/commands/install_uninstall.py
@@ -71,6 +71,7 @@ def install(
             sys_executable=sys.executable,
             hook_type=hook_type,
             hook_specific=hook_specific_contents,
+            config_file=runner.config_file,
             skip_on_missing_conf=skip_on_missing_conf,
         )
         pre_commit_file_obj.write(contents)
diff --git a/pre_commit/resources/commit-msg-tmpl b/pre_commit/resources/commit-msg-tmpl
index b11521b0..182f214a 100644
--- a/pre_commit/resources/commit-msg-tmpl
+++ b/pre_commit/resources/commit-msg-tmpl
@@ -1 +1 @@
-args="run --hook-stage=commit-msg --commit-msg-filename=$1"
+args="--hook-stage=commit-msg --commit-msg-filename=$1"
diff --git a/pre_commit/resources/hook-tmpl b/pre_commit/resources/hook-tmpl
index 3bfce5c7..78aa2a83 100644
--- a/pre_commit/resources/hook-tmpl
+++ b/pre_commit/resources/hook-tmpl
@@ -38,13 +38,13 @@ if [ -x "$HERE"/{hook_type}.legacy ]; then
     fi
 fi
 
-CONF_FILE=$(git rev-parse --show-toplevel)"/.pre-commit-config.yaml"
+CONF_FILE=$(git rev-parse --show-toplevel)"/{config_file}"
 if [ ! -f $CONF_FILE  ]; then
     if [ $SKIP_ON_MISSING_CONF = true ] || [ ! -z $PRE_COMMIT_ALLOW_NO_CONFIG ]; then
-        echo '`.pre-commit-config.yaml` config file not found. Skipping `pre-commit`.'
+        echo '`{config_file}` config file not found. Skipping `pre-commit`.'
         exit $retv
     else
-        echo 'No .pre-commit-config.yaml file was found'
+        echo 'No {config_file} file was found'
         echo '- To temporarily silence this, run `PRE_COMMIT_ALLOW_NO_CONFIG=1 git ...`'
         echo '- To permanently silence this, install pre-commit with the `--allow-missing-config` option'
         echo '- To uninstall pre-commit run `pre-commit uninstall`'
@@ -56,7 +56,7 @@ fi
 
 # Run pre-commit
 if ((WHICH_RETV == 0)); then
-    pre-commit $args
+    pre-commit run $args -c {config_file}
     PRE_COMMIT_RETV=$?
 elif ((ENV_PYTHON_RETV == 0)); then
     "$ENV_PYTHON" -m pre_commit.main $args
diff --git a/pre_commit/resources/pre-push-tmpl b/pre_commit/resources/pre-push-tmpl
index 81d0dcbe..f866eeff 100644
--- a/pre_commit/resources/pre-push-tmpl
+++ b/pre_commit/resources/pre-push-tmpl
@@ -9,14 +9,14 @@ do
                 # Check that the ancestor has at least one parent
                 git rev-list --max-parents=0 "$local_sha" | grep "$first_ancestor" > /dev/null
                 if [ $? -ne 0 ]; then
-                    args="run --all-files"
+                    args="--all-files"
                 else
                     source=$(git rev-parse "$first_ancestor"^)
-                    args="run --origin $local_sha --source $source"
+                    args="--origin $local_sha --source $source"
                 fi
             fi
         else
-            args="run --origin $local_sha --source $remote_sha"
+            args="--origin $local_sha --source $remote_sha"
         fi
     fi
 done
diff --git a/tests/commands/install_uninstall_test.py b/tests/commands/install_uninstall_test.py
index 94d396a9..357131c5 100644
--- a/tests/commands/install_uninstall_test.py
+++ b/tests/commands/install_uninstall_test.py
@@ -57,6 +57,7 @@ def test_install_pre_commit(tempdir_factory):
         sys_executable=sys.executable,
         hook_type='pre-commit',
         hook_specific='',
+        config_file=runner.config_file,
         skip_on_missing_conf='false',
     )
     assert pre_commit_contents == expected_contents
@@ -72,6 +73,7 @@ def test_install_pre_commit(tempdir_factory):
         sys_executable=sys.executable,
         hook_type='pre-push',
         hook_specific=pre_push_template_contents,
+        config_file=runner.config_file,
         skip_on_missing_conf='false',
     )
     assert pre_push_contents == expected_contents