Biokepi API : Biokepi.EDSL

struct

(** The definition of the Embedded DSL *)


  module type Semantics = Biokepi_pipeline_edsl.Semantics.Bioinformatics_base

(** Various compilers to “interpret” the EDSL. *)


  module Compile = struct

(** Compiler to SmartPrint.t displayable pseudo code, see the smart-print library. *)


    module To_display = Biokepi_pipeline_edsl.To_display

(** Compiler to Ketrew workflows using the Biokepi.Tools implementations.

The compiler is itself a functor, see the example:

          let module Workflow_compiler =
            Biokepi.EDSL.Compile.To_workflow.Make(struct
              let processors = 42
              let work_dir = "/work/dir/"
              let machine =
                Biokepi.Setup.Build_machine.create
                  "ssh://example.com/tmp/KT/"
            end)
          in
          let module Ketrew_pipeline_1 = Pipeline_1(Workflow_compiler) in


    module To_workflow = Biokepi_pipeline_edsl.To_workflow

(** Compiler to JSON (Yojson.Basic.t). *)


    module To_json : Biokepi_pipeline_edsl.Semantics.Bioinformatics_base
      with type 'a repr = var_count: int -> Yojson.Basic.json
       and
       type 'a observation = Yojson.Basic.json =
      Biokepi_pipeline_edsl.To_json

(** Compiler to DOT graph descriptions. *)


    module To_dot : sig
      include Biokepi_pipeline_edsl.Semantics.Bioinformatics_base
        with
          type 'a repr = var_count:int -> Biokepi_pipeline_edsl.To_dot.Tree.t
         with type 'a observation =
            parameters: Biokepi_pipeline_edsl.To_dot.parameters -> SmartPrint.t
      type parameters = Biokepi_pipeline_edsl.To_dot.parameters = {
        color_input:
          name: string -> attributes: (string * string) list -> string option;
      }
      val default_parameters : parameters
    end = Biokepi_pipeline_edsl.To_dot

  end

(** Transformations on the EDSL. *)


  module Transform = struct

(** Apply as much EDSL functions as possible to their arguments (including list_map). *)


    module Apply_functions = Biokepi_pipeline_edsl.Transform_applications.Apply

  end

(** Library of reusable pieces of pipeline. *)


  module Library = Biokepi_pipeline_edsl.Pipeline_library

end