convergence_detection.ml

open Bistro.EDSL
open Bistro.Std
open Core
open File_formats
open Bistro_bioinfo.Std

type pcoc_out
type diffsel_out

type det_out =
  | Pcoc_out
  | Diffsel_out

let pcoc ?gamma  ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) :  (*`pcoc*) det_out directory workflow =
  let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"06212018" () in
  workflow ~descr:"convergence_detection.pcoc" [
    cmd "pcoc_det.py" ~env [
        opt "-t" dep tree;
        opt "-m" string "-";
        opt "-aa"  dep faa ;
        opt "-o"  ident dest ;
        option ( flag string "--gamma" ) gamma;
    ]
  ]


let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) :  (*`diffsel*) det_out directory workflow =
  let env = docker_image ~account:"vlanore" ~name:"diffsel" ~tag:"v1.0" () in
  (*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
  workflow ~descr:"convergence_detection.diffsel" [
    mkdir_p dest;
    cmd "_build/diffsel" ~env [
        opt "-t" dep tree;
        opt "-d"  dep phy_n ;
        opt "-ncond"  int 2 ;
        opt "-x" seq [ int w_every; string " "; int n_cycles];
        seq [ ident dest ; string "/myrun"] ;
    ]
  ]