Gemma univariate LMM call as Bistro workflow

lib/gemma.ml

@@ -34,6 +34,30 @@ let%pworkflow phenotype_of_tree nhx =
   in
   Out_channel.with_file [%dest] ~f:(write_phenotypes leaves)
 
+let template_of_lmm lmm = 
+  int (
+    match lmm with 
+    | `Wald   -> 1
+    | `LRT    -> 2
+    | `Score  -> 3
+    | `All    -> 4
+  )
+
+let univariate_lmm ~lmm ~genotype ~phenotype ~relatedness_matrix = 
+  Workflow.shell ~descr:"gemma.univariate_lmm" [
+    cmd "gemma" [
+      opt "-g" dep genotype ;
+      opt "-p" dep phenotype ;
+      opt "-lmm" template_of_lmm lmm ;
+      opt "-k" dep relatedness_matrix ;
+      opt "-outdir" Fn.id tmp ;
+    ] ; 
+    cmd "cp" [
+      tmp // "result.assoc.txt" ;
+      dest ;
+    ] ;
+  ]
+  
 let template_of_mode m =
   int (
     match m with

lib/gemma.mli

@@ -14,3 +14,10 @@ val calculate_relatedness_matrix :
   genotype:bimbam file ->
   phenotype:bimbam file ->
   relatedness_matrix file 
+
+val univariate_lmm : 
+  lmm:[`Wald | `LRT | `Score | `All ] ->
+  genotype: bimbam file ->
+  phenotype: bimbam file ->
+  relatedness_matrix: relatedness_matrix file -> 
+  text file
\ No newline at end of file