Module Biokepi_run_environment.Machine (.ml)

module Machine: sig .. end

module Tool: sig .. end

module Make_fun: sig .. end

Jobs in Biokepi ask the computing environment (defined below in Biokepi_run_environment.Machine) for resources.

type t = {

	`name : string;`
	`host : Common.KEDSL.Host.t;`
	`pyensembl_cache_dir : string option;`
	`get_reference_genome : string -> Reference_genome.t;`
	`toolkit : Tool.Kit.t;`
	`run_program : Make_fun.t;`
	`work_dir : string;`
	`max_processors : int;`

}

val create : host:Common.KEDSL.Host.t ->
       ?pyensembl_cache_dir:string ->
       get_reference_genome:(string -> Reference_genome.t) ->
       toolkit:Tool.Kit.t ->
       run_program:Make_fun.t ->
       work_dir:string ->
       max_processors:int -> string -> t

val name : t -> string

val as_host : ?with_shell:string ->
       t -> Common.KEDSL.Host.t

val get_pyensembl_cache_dir : t -> string option

val get_reference_genome : t -> string -> Reference_genome.t

val get_tool : t ->
       Tool.Definition.t ->
       Tool.Kit.tool

val run_program : t ->
       Make_fun.t

val max_processors : t -> int

Get the maximum number of processors that a single job can use in the Machine.t (i.e. usually the “number-of-threads” paramters of most tools)

val quick_run_program : t ->
       Make_fun.t

val run_stream_processor : ?self_ids:string list ->
       t ->
       Make_fun.t

Run a program that does not use much memory and runs on one core.

val run_download_program : t ->
       Make_fun.t

Run a program that does not use much memory, runs on one core, and needs the internet.

val run_big_program : t ->
       ?processors:int ->
       ?self_ids:string list -> Make_fun.t

val work_dir : t -> string