diff --git a/Jenkinsfile b/Jenkinsfile
index d84a2bf..97e754d 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -11,6 +11,10 @@ pipeline {
             parallel {
                 stage("recipes repo") {
                     steps {
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
+                        sh 'git submodule init'
+                        sh 'git submodule update'
                         dir('auto-updated-bioconda-recipes') {
                             sh 'git checkout update-autobigs-engine'
                         }