set up basic CLI

app/reviewphiltrans_app.ml

+open Core
+open Reviewphiltrans
+
+let () =
+  Command.group ~summary:"Reviewphiltrans" [
+    "pipeline", Pipeline.command ;
+  ]
+  |> Command.run

lib/pipeline.ml

+open Core
 open Bistro_utils
 
-let repo = Repo.[
+let repo () = Repo.[
   ]
+
+let main ~outdir ?np ?mem ~preview_mode () =
+  ()
+
+let command =
+  let open Command.Let_syntax in
+  Command.basic
+    ~summary:"Run simulation pipeline"
+    [%map_open
+      let outdir =
+        flag "--outdir"  (optional string) ~doc:"PATH Output directory"
+      and preview_mode =
+        flag "--preview-mode" (optional int) ~doc:"INT If present, only consider K million reads"
+      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
+      main ~outdir ?np ?mem ~preview_mode
+    ]