diff options
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 21 |
1 files changed, 21 insertions, 0 deletions
diff --git a/README.md b/README.md index 2369f4e..3239ab9 100644 --- a/README.md +++ b/README.md @@ -46,8 +46,29 @@ WIP ## 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. |