utils: new R script module

lib/utils/r_script.ml

@@ -0,0 +1,60 @@
+open Base
+open Bistro
+open Bistro.Template_dsl
+
+type t = template
+
+type expr = t
+
+type arg = t
+
+let make xs = Template_dsl.(seq ~sep:"\n" xs)
+
+let source s = Template_dsl.string s
+
+let dest = Template_dsl.(quote ~using:'"' dest)
+
+let tmp = Template_dsl.(quote ~using:'"' tmp)
+
+let string s =
+  Template_dsl.(quote ~using:'"' (string s))
+
+let int i = Template_dsl.int i
+
+let float f = Template_dsl.float f
+
+let dep w = Template_dsl.(quote ~using:'"' (dep w))
+
+let call_gen fn arg xs  =
+  let open Template_dsl in
+  seq ~sep:"" [
+    string fn ;
+    string "(" ;
+    list ~sep:"," arg xs ;
+    string ")" ;
+  ]
+
+let call fn args = call_gen fn Fn.id args
+
+let vector f xs = call_gen "c" f xs
+
+let ints xs = vector Template_dsl.int xs
+let floats xs = vector Template_dsl.float xs
+let strings xs = vector string xs
+let deps xs = vector dep xs
+
+let arg ?l e =
+  let open Template_dsl in
+  match l with
+  | None -> e
+  | Some label ->
+    seq ~sep:"" [ string label ; string "=" ; e ]
+
+let assign var e =
+  let open Template_dsl in
+  seq ~sep:" " [ string var ; string "<-" ; e ]
+
+let workflow ?descr ?np ?mem ?img exprs =
+  Workflow.shell ?descr ?np ?mem Shell_dsl.[
+    cmd "Rscript" ?img [ file_dump (make exprs) ] ;
+  ]

lib/utils/r_script.mli

@@ -0,0 +1,32 @@
+open Bistro
+open Bistro.Template_dsl
+
+type t
+type expr
+type arg
+
+
+val make : expr list -> template
+
+val dest : expr
+val tmp : expr
+val source : string -> expr
+val call : string -> arg list -> expr
+val string : string -> expr
+val int : int -> expr
+val float : float -> expr
+val dep : _ pworkflow -> expr
+val ints : int list -> expr
+val floats : float list -> expr
+val strings : string list -> expr
+val deps : _ pworkflow list -> expr
+val arg : ?l:string -> expr -> arg
+val assign : string -> expr -> expr
+
+val workflow :
+  ?descr:string ->
+  ?np:int ->
+  ?mem:int workflow ->
+  ?img:Shell_dsl.container_image list ->
+  expr list ->
+  'a pworkflow