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Commit c2f56eac authored by Louis Duchemin's avatar Louis Duchemin
Browse files

Gemma univariate LMM call as Bistro workflow

parent c67a3c8f
......@@ -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
......
......@@ -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
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