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 ## Run GEMMA
 
+Pangemma (for now) maintains a version of gemma and may support new features. Run the legacy version with:
+
+```
+gemma -h
+# compute Kinship matrix
+gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt \
+    -gk -o mouse_hs1940
+# run univariate LMM
+gemma -g ./example/mouse_hs1940.geno.txt.gz \
+    -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt \
+    -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm
+```
+
 ### Debugging and optimization
 
+We use guix for debugging and development. Try something like
+
+```
+LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib gdb --args  ./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz \
+    -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt \
+    -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm
+```
+
 ## Citing PanGEMMA
 
 PanGEMMA is not published yet.