diff --git a/pipeline/prepareCatalogs.py b/pipeline/prepareCatalogs.in.py
similarity index 99%
rename from pipeline/prepareCatalogs.py
rename to pipeline/prepareCatalogs.in.py
index 8d766b4..b6f79a0 100755
--- a/pipeline/prepareCatalogs.py
+++ b/pipeline/prepareCatalogs.in.py
@@ -90,8 +90,8 @@ endCatalogStage   = 4
 startAPStage = 1
 endAPStage = 7
 
-ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
-CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
+ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/"
+CTOOLS_PATH = "@CMAKE_BINARY_DIR@/c_tools/"
 freshStack = True
 errorBars = "CALCULATED"
 numIncoherentRuns = 100