: sig
(** Simplified creation of Run_environment.Machine.t values *)
open Biokepi_run_environment open Common
(** Build a Run_environment.Machine.t with convenient default values.

The string argument is a URI like the one expected by Ketrew.EDSL.Host.parse except that the “path” is the meta-playground for Biokepi (the ketrew playground will be (meta_playground // "ketrew_playground").

The default run_program is daemonizing with `Python_daemon.

The default toolkit is default_toolkit from Tool_providers. This machine will get tools installations and data-fetching from Biokepi's defaults. The ?b37 argument allows to override the locations of the “B37” genome; to override other default please use Run_environment.Machine.create directly. *)

val create :   ?max_processors : int ->   ?gatk_jar_location:(unit -> Workflow_utilities.Download.tool_file_location) ->   ?mutect_jar_location:(unit -> Workflow_utilities.Download.tool_file_location) ->   ?netmhc_tool_locations:(unit -> Netmhc.netmhc_file_locations) ->   ?pyensembl_cache_dir:string ->   ?run_program:Machine.Make_fun.t ->   ?toolkit:Machine.Tool.Kit.t ->   ?b37:Reference_genome.t ->   string ->   Machine.t end  = struct open Biokepi_run_environment open Common let default_run_program : host:KEDSL.Host.t -> Machine.Make_fun.t =   fun ~host ?(name="biokepi-ssh-box") ?(requirements = []) program ->     let open KEDSL in     daemonize ~using:`Python_daemon ~host program let create     ?(max_processors = 1)     ?gatk_jar_location     ?mutect_jar_location     ?netmhc_tool_locations     ?pyensembl_cache_dir     ?run_program ?toolkit ?b37 uri =   let open KEDSL in   let host = Host.parse (uri // "ketrew_playground") in   let meta_playground = Uri.of_string uri |> Uri.path in   let run_program =     match run_program with     | None -> default_run_program ~host     | Some r -> r   in   let toolkit =     Option.value toolkit       ~default:(Tool_providers.default_toolkit ()                   ~run_program                   ~host ~install_tools_path:(meta_playground // "install-tools")                   ?gatk_jar_location ?mutect_jar_location                   ?netmhc_tool_locations)   in   Machine.create (sprintf "ssh-box-%s" uri)     ~max_processors     ?pyensembl_cache_dir     ~get_reference_genome:(fun name ->         match name, b37 with         | name, Some some37 when name = Reference_genome.name some37 -> some37         | name, _ ->                   Download_reference_genomes.get_reference_genome name             ~toolkit ~host ~run_program             ~destination_path:(meta_playground // "reference-genome"))     ~host     ~toolkit     ~run_program     ~work_dir:(meta_playground // "work") end