Module Biokepi_environment_setup.Netmhc (.ml)

module Netmhc: sig .. end

val rm_path : host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       string ->
       < is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option >
       Biokepi_run_environment.Common.KEDSL.workflow_node

type netmhc_file_locations = {

val escape_char : needle:char -> string -> string

val replace_value : string -> string -> string -> Biokepi_run_environment.Common.KEDSL.Program.t

val replace_env_value : string -> string -> string -> Biokepi_run_environment.Common.KEDSL.Program.t

val extract_location : [< `Fail of 'a | `Scp of string | `Wget of string ] -> string

val guess_major_version : [< `Fail of 'a | `Scp of string | `Wget of string ] -> char option

val guess_folder_name : [< `Fail of 'a | `Scp of string | `Wget of string ] -> string

val tmp_dir : string -> string

val netmhc_conda_env : string -> Biokepi_environment_setup.Conda.conda_environment_type

val netmhc_runner_path : string -> string

val netmhc_runner_script_contents : binary_name:'a ->
       binary_path:string ->
       conda_env:Biokepi_environment_setup.Conda.conda_environment_type -> string

val create_netmhc_runner_cmd : binary_name:'a ->
       binary_path:string ->
       conda_env:Biokepi_environment_setup.Conda.conda_environment_type ->
       string -> Biokepi_run_environment.Common.KEDSL.Program.t

val default_netmhc_install : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_path:string ->
       tool_file_loc:[< `Fail of 'a & 'b & string | `Scp of string | `Wget of string ] ->
       binary_name:string ->
       example_data_file:string option ->
       env_setup:[< `ENV of string * string | `GENERIC of string * string ] list ->
       ?depends:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
                  .. >
                Biokepi_run_environment.Common.KEDSL.workflow_node list ->
       ?data_folder_name:string ->
       ?data_folder_dest:string ->
       unit ->
       Biokepi_run_environment.Machine.Tool.t * string *
       < exists : Ketrew_pure.Target.Condition.t;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string >
       Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val guess_env_setup : install_path:string ->
       ?tmp_dirname:string ->
       ?home_env:string ->
       [< `Fail of 'a | `Scp of string | `Wget of string ] ->
       [> `ENV of string * string ] list

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