app/Reviewphiltrans: switch to new real data pipeline

app/reviewphiltrans_app.ml

 open Core
 open Reviewphiltrans
 
+let first_nhx_in_dir dir =
+  Sys.readdir dir
+  |> Array.find_exn ~f:(String.is_suffix ~suffix:".nhx")
+
+let realdata_main ~indir ~outdir ~np ~mem () =
+  let mem = Option.map mem ~f:(fun i -> `GB i) in
+  let rd =
+    Real_dataset.make
+      ~alignment_dir_path:(Filename.concat indir "Alignments")
+      ~tree_path:(Filename.concat indir (first_nhx_in_dir indir))
+  in
+  Real_dataset.repo [`Multinomial] rd
+  |> Bistro_utils.Repo.build_main ~outdir ?np ?mem
+
+let realdata_command =
+  let open Command.Let_syntax in
+  Command.basic
+    ~summary:"Run pipeline on real data"
+    [%map_open
+      let outdir =
+        flag "--outdir" (required string) ~doc:"PATH Output directory"
+      and indir =
+        flag "--indir" (required string) ~doc:"PATH Input directory"
+      (* and preview =
+       *   flag "--preview-mode" no_arg ~doc:" Preview mode"
+       * and use_diffsel =
+       *   flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
+       * and use_c60 =
+       *   flag "--c60" no_arg ~doc:" use the pcoc c60 method (slow)."
+       * and calc_dnds =
+       *   flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)." *)
+      and np =
+        flag "--np" (optional int) ~doc:"INT Number of available processors"
+      and mem =
+        flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
+      in
+      realdata_main ~indir ~outdir ~np ~mem
+    ]
+
 let () =
   Command.group ~summary:"Reviewphiltrans" [
     "validation", Pipeline.validation_command ;