sig
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 = {
netmhc :
Biokepi_run_environment.Workflow_utilities.Download.tool_file_location;
netmhcpan :
Biokepi_run_environment.Workflow_utilities.Download.tool_file_location;
pickpocket :
Biokepi_run_environment.Workflow_utilities.Download.tool_file_location;
netmhccons :
Biokepi_run_environment.Workflow_utilities.Download.tool_file_location;
}
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:Biokepi_environment_setup.Netmhc.netmhc_file_locations ->
unit -> Biokepi_run_environment.Machine.Tool.Kit.t
end