diff --git a/moulin/builders/custom_script.py b/moulin/builders/custom_script.py
index d187d14..0764ae7 100644
--- a/moulin/builders/custom_script.py
+++ b/moulin/builders/custom_script.py
@@ -10,6 +10,7 @@
 import os.path
 from typing import List
 from moulin.yaml_wrapper import YamlValue
+from moulin.utils import construct_fetcher_dep_cmd
 from moulin import ninja_syntax
 
 
@@ -26,9 +27,12 @@ def gen_build_rules(generator: ninja_syntax.Writer):
     Generate custom_script build rules for ninja
     """
     cmd = " && ".join([
+        # Generate fetcher dependency file
+        construct_fetcher_dep_cmd(),
+        "cd $build_dir",
         "( [ -d $work_dir ] || mkdir $work_dir )",
-        "echo '# Code generated by moulin. All manual changes will be lost' > $work_dir/$config_file",
-        "echo $b64config | base64 -d - >> $work_dir/$config_file",
+        "echo '# Code generated by moulin. All manual changes will be lost' > $config_file",
+        "echo $b64config | base64 -d - >> $config_file",
     ])
     generator.rule("cs_update_conf",
                    command=cmd,
@@ -36,7 +40,8 @@ def gen_build_rules(generator: ninja_syntax.Writer):
     generator.newline()
 
     cmd = " && ".join([
-        "$script $args $work_dir/$config_file"
+        "cd $build_dir",
+        "$script $args $config_file"
     ])
     generator.rule("cs_build",
                    command=cmd,
@@ -65,9 +70,11 @@ def gen_build(self):
         common_variables = {
             "script": self.conf["script"].as_str,
             "work_dir": work_dir,
+            "build_dir": self.build_dir,
+            "name": self.name,
         }
-        local_conf_file = f"conf-{self.name}.yaml"
-        local_conf_target = os.path.join(work_dir, local_conf_file)
+        local_conf_file = os.path.join(work_dir, f"conf-{self.name}.yaml")
+        local_conf_target = os.path.join(self.build_dir, local_conf_file)
         serialized_conf = yaml.serialize(self.conf._node)
         conf_bytes = serialized_conf.encode("utf-8")
         b64bytes = base64.b64encode(conf_bytes)