wf.ml

#use "topfind"
#thread
#require "nonstd"
#require "hamkepi"
#require "ketrew"
#require "biokepi"




module Demeter = Hamkepi.Demeter.Of_ssh(struct
    let username = "hodesi01"
    let ssh_name = "demeter"
    let gatk_jar_location =
      `Wget "http://wr.mondet.org/smondet/not_really_private/GenomeAnalysisTK.jar"
    let mutect_jar_location =
      `Wget "http://wr.mondet.org/smondet/not_really_private/muTect-1.1.6-10b1ba92.jar"
    let playground =
      Nonstd.sprintf "/demeter/scratch/%s/ksinai-demeter" username
  end)

let run_command_with_demeter cmd =
  let module KEDSL = Ketrew.EDSL in
  let host = Demeter.host
  in
  let program = KEDSL.Program.sh cmd in
  let demeter_build_process =
    KEDSL.yarn_distributed_shell
      ~host ~timeout:(`Seconds 180) ~container_memory:(`GB 1) ~application_name:"isaac_ketrew_demeter_sheller"
      program
  in
  KEDSL.target
     "run_command_with_demeter"
     ~make:demeter_build_process

let () =
  let workflow = run_command_with_demeter Sys.argv.(1) in
  Ketrew.Client.submit workflow