Module Biokepi_environment_setup.Biopam (.ml)

module Biopam: sig .. end

Provide tools via Biopam: https://github.com/solvuu/biopam

type tool_type = [ `Application | `Library of string ]

type install_target = {

`definition : Biokepi_run_environment.Machine.Tool.Definition.t;`
`tool_type : tool_type;`
`package : string;`	`(*`	What do we call 'install opam ' with	`*)`
`witness : string;`	`(*`	File that must exist after install, ex: bowtie exec picard.jar	`*)`
`test : (host:Biokepi_run_environment.Common.KEDSL.Host.t -> string -> Biokepi_run_environment.Common.KEDSL.Command.t) option;`
`edges : Biokepi_run_environment.Common.KEDSL.workflow_edge list;`
`init_environment : install_path:string -> Biokepi_run_environment.Common.KEDSL.Program.t;`
`requires_conda : bool;`
repository : [ `Biopam \| `Custom of string \| `Opam ];
`compiler : string option;`
`pin : string option;`

}

val install_target : ?tool_type:tool_type ->
       ?test:(host:Biokepi_run_environment.Common.KEDSL.Host.t ->
              string -> Biokepi_run_environment.Common.KEDSL.Command.t) ->
       ?edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       ?init_environment:(install_path:string ->
                          Biokepi_run_environment.Common.KEDSL.Program.t) ->
       ?requires_conda:bool ->
       witness:string ->
       ?package:string ->
       ?repository:[ `Biopam | `Custom of string | `Opam ] ->
       ?compiler:string ->
       ?pin:string ->
       Biokepi_run_environment.Machine.Tool.Definition.t ->
       install_target

val default_opam_url : string

val default_biopam_url : string

val provide : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_path:string ->
       install_target ->
       Biokepi_run_environment.Machine.Tool.t

val default : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_path:string -> unit -> Biokepi_run_environment.Machine.Tool.Kit.t