diff --git a/cobrexa.def b/cobrexa.def
index b04fcc671591b9b6af1027239848d808a794a1d0..54b376f8bc5f66c5a253f8341b44989f7784c010 100644
--- a/cobrexa.def
+++ b/cobrexa.def
@@ -2,7 +2,7 @@ Bootstrap: library
 From: cylon-x/lcsb-biocore/julia-base:latest
 
 %setup
-    cp -a `pwd` ${SINGULARITY_ROOTFS}/project/
+    GIT_DIR=`pwd`/.git GIT_WORK_TREE=${SINGULARITY_ROOTFS}/project/ git checkout -f
 
 %post
     export JULIA_DEPOT_PATH=/user/.julia