Commit 057f45bd authored by Philippe Veber's avatar Philippe Veber
Browse files

app/Reviewphiltrans: switch to new real data pipeline

parent ac2adfb0
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 = mem ~f:(fun i -> `GB i) in
let rd =
~alignment_dir_path:(Filename.concat indir "Alignments")
~tree_path:(Filename.concat indir (first_nhx_in_dir indir))
Real_dataset.repo [`Multinomial] rd
|> Bistro_utils.Repo.build_main ~outdir ?np ?mem
let realdata_command =
let open Command.Let_syntax in
~summary:"Run pipeline on real data"
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)"
realdata_main ~indir ~outdir ~np ~mem
let () = ~summary:"Reviewphiltrans" [
"validation", Pipeline.validation_command ;
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