sig
module Host = Ketrew.EDSL.Host
module Program = Ketrew.EDSL.Program
module Condition = Ketrew.EDSL.Condition
module Build_process = Ketrew.EDSL.Build_process
val daemonize :
?starting_timeout:float ->
?call_script:(string -> string list) ->
?using:[ `Nohup_setsid | `Python_daemon ] ->
?host:Host.t -> ?no_log_is_ok:bool -> Program.t -> Build_process.t
val lsf :
?host:Host.t ->
?queue:string ->
?name:string ->
?wall_limit:string ->
?processors:[ `Min of int | `Min_max of int * int ] ->
?project:string ->
?request_memory:[ `GB of int | `MB of int ] ->
?raw_options:string list -> Program.t -> Build_process.t
val pbs :
?host:Host.t ->
?queue:string ->
?name:string ->
?wall_limit:[ `Hours of float ] ->
?processors:int ->
?email_user:[ `Always of string | `Never ] ->
?shell:string -> Program.t -> Build_process.t
val yarn_application :
?host:Host.t ->
?daemonize_using:[ `Nohup_setsid | `Python_daemon ] ->
?daemon_start_timeout:float -> Program.t -> Build_process.t
val yarn_distributed_shell :
?host:Host.t ->
?daemonize_using:[ `Nohup_setsid | `Python_daemon ] ->
?daemon_start_timeout:float ->
?hadoop_bin:string ->
?distributed_shell_shell_jar:string ->
?container_vcores:int ->
container_memory:[ `GB of int | `MB of int | `Raw of string ] ->
timeout:[ `Raw of string | `Seconds of int ] ->
application_name:string -> Program.t -> Build_process.t
module Internal_representation = Ketrew.EDSL.Internal_representation
type 'a product = 'a constraint 'a = < is_done : Condition.t option; .. >
type 'a workflow_node =
< product : 'a product; render : Internal_representation.t >
constraint 'a = < is_done : Condition.t option; .. >
type workflow_edge = Ketrew.EDSL.workflow_edge
val depends_on :
< is_done : Condition.t option; .. > workflow_node -> workflow_edge
val on_success_activate :
< is_done : Condition.t option; .. > workflow_node -> workflow_edge
val on_failure_activate :
< is_done : Condition.t option; .. > workflow_node -> workflow_edge
type ensures_option =
[ `Is_verified of Condition.t | `Nothing | `Product_is_done ]
val workflow_node :
?name:string ->
?active:bool ->
?make:Build_process.t ->
?ensures:ensures_option ->
?metadata:[ `String of string ] ->
?equivalence:Ketrew_pure.Target.Equivalence.t ->
?tags:string list ->
?edges:workflow_edge list ->
(< is_done : Condition.t option; .. > as 'a) product -> 'a workflow_node
type not_already_done = < is_done : Condition.t option >
val without_product : not_already_done
type single_file =
< exists : Ketrew_pure.Target.Condition.t; host : Host.t;
is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
is_done : Ketrew_pure.Target.Condition.t option; path : string >
val single_file : ?host:Host.t -> string -> single_file product
type list_of_files =
< is_done : Ketrew_pure.Target.Condition.t option;
paths : string list >
val list_of_files : ?host:Host.t -> string list -> list_of_files product
type unknown_product = < is_done : Condition.t option >
val forget_product :
< is_done : Condition.t option; .. > workflow_node ->
unknown_product workflow_node
val workflow_to_string :
?ansi_colors:bool ->
?indentation:int ->
< is_done : Condition.t option; .. > workflow_node -> string
val add_tags :
?recursive:bool ->
< is_done : Condition.t option; .. > workflow_node -> string list -> unit
val node_id : < is_done : Condition.t option; .. > workflow_node -> string
val node_name :
< is_done : Condition.t option; .. > workflow_node -> string
class type user_artifact =
object
method exists : Ketrew_pure.Target.Condition.t
method is_bigger_than : int -> Ketrew_pure.Target.Condition.t
method path : string
end
val file : ?host:Host.t -> string -> user_artifact
val unit : user_artifact
class type user_target =
object
method activate : unit
method add_recursive_tags : string list -> unit
method add_tags : string list -> unit
method depends_on : user_target list
method get_recursive_tags : string list
method id : Ketrew_pure.Internal_pervasives.Unique_id.t
method is_active : bool
method metadata : [ `String of string ] option
method name : string
method on_failure_activate : user_target list
method on_success_activate : user_target list
method product : user_artifact
method render : Ketrew_pure.Target.t
end
val to_display_string :
?ansi_colors:bool -> ?indentation:int -> user_target -> string
module Command = Ketrew_pure.Target.Command
type nothing = < is_done : Condition.t option >
val nothing : < is_done : 'a option >
val target : 'a -> [> `Please_KEDSL_workflow ]
val file_target : 'a -> [> `Please_KEDSL_workflow ]
type file_workflow = single_file workflow_node
type phony_workflow =
Biokepi_run_environment.Common.KEDSL.nothing workflow_node
type fastq_reads =
< escaped_sample_name : string; fragment_id : string option;
fragment_id_forced : string;
is_done : Ketrew_pure.Target.Condition.t option;
paths : string * string option; r1 : single_file;
r2 : single_file option; sample_name : string >
val fastq_reads :
?host:Host.t ->
?name:string ->
?fragment_id:string ->
string ->
string option -> Biokepi_run_environment.Common.KEDSL.fastq_reads
val transform_fastq_reads :
?name:string ->
?fragment_id:string option ->
Biokepi_run_environment.Common.KEDSL.fastq_reads ->
string ->
string option -> Biokepi_run_environment.Common.KEDSL.fastq_reads
val read_1_file_node :
Biokepi_run_environment.Common.KEDSL.fastq_reads workflow_node ->
< exists : Ketrew_pure.Target.Condition.t; host : Host.t;
is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
is_done : Condition.t option; path : string >
workflow_node
val read_2_file_node :
Biokepi_run_environment.Common.KEDSL.fastq_reads workflow_node ->
< exists : Ketrew_pure.Target.Condition.t; host : Host.t;
is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
is_done : Condition.t option; path : string >
workflow_node option
val fastq_node_of_single_file_nodes :
host:Host.t ->
name:string ->
?fragment_id:string ->
< is_done : Condition.t option; path : string; .. > product workflow_node ->
< is_done : Condition.t option; path : string; .. > workflow_node option ->
< escaped_sample_name : string; fragment_id : string option;
fragment_id_forced : string; is_done : Condition.t option;
paths : string * string option; r1 : single_file;
r2 : single_file option; sample_name : string >
workflow_node
val transform_single_file :
path:string -> < host : Host.t; .. > -> single_file product
type bam_file =
< escaped_sample_name : string; host : Host.t;
is_done : Ketrew_pure.Target.Condition.t option; path : string;
reference_build : string; sample_name : string;
sorting : [ `Coordinate | `Read_name ] option >
val bam_file :
host:Host.t ->
?name:string ->
?sorting:[ `Coordinate | `Read_name ] ->
reference_build:string ->
string -> Biokepi_run_environment.Common.KEDSL.bam_file
val transform_bam :
?change_sorting:[ `Coordinate | `Read_name ] ->
Biokepi_run_environment.Common.KEDSL.bam_file ->
path:string -> Biokepi_run_environment.Common.KEDSL.bam_file
type bam_list =
< bams : Biokepi_run_environment.Common.KEDSL.bam_file list;
is_done : Ketrew_pure.Target.Condition.t option >
val bam_list :
Biokepi_run_environment.Common.KEDSL.bam_file list ->
Biokepi_run_environment.Common.KEDSL.bam_list
val explode_bam_list_node :
Biokepi_run_environment.Common.KEDSL.bam_list workflow_node ->
< escaped_sample_name : string; host : Host.t;
is_done : Condition.t option; path : string; reference_build :
string; sample_name : string;
sorting : [ `Coordinate | `Read_name ] option >
workflow_node list
type _ bam_or_bams =
Single_bam :
Biokepi_run_environment.Common.KEDSL.bam_file workflow_node ->
Biokepi_run_environment.Common.KEDSL.bam_file workflow_node
Biokepi_run_environment.Common.KEDSL.bam_or_bams
| Bam_workflow_list :
Biokepi_run_environment.Common.KEDSL.bam_file workflow_node list ->
Biokepi_run_environment.Common.KEDSL.bam_list workflow_node
Biokepi_run_environment.Common.KEDSL.bam_or_bams
type vcf_file =
< as_single_file : single_file product; host : Host.t;
is_done : Ketrew_pure.Target.Condition.t option; path : string;
reference_build : string >
val vcf_file :
host:Host.t ->
reference_build:string ->
string -> Biokepi_run_environment.Common.KEDSL.vcf_file
val transform_vcf :
< host : Host.t; reference_build : string; .. > ->
path:string -> Biokepi_run_environment.Common.KEDSL.vcf_file
val submit :
< is_done : Ketrew.EDSL.Condition.t option; .. > Ketrew.EDSL.product
Ketrew.EDSL.workflow_node -> unit
end