Module Biokepi_environment_setup.Tool_providers (.ml)

module Tool_providers: 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

val generic_installation : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_path:string ->
       install_program:Biokepi_run_environment.Common.KEDSL.Program.t ->
       witness:(< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
                  .. >
                as 'a)
               Biokepi_run_environment.Common.KEDSL.product ->
       url:string ->
       ?unarchived_directory:string ->
       string -> 'a Biokepi_run_environment.Common.KEDSL.workflow_node

module Tool_def: Biokepi_run_environment.Machine.Tool.Definition

type installable = {

	`tool_definition : Tool_def.t;`
	`url : string;`
	`install_program : path:string -> Biokepi_run_environment.Common.KEDSL.Program.t;`
	`init_program : path:string -> Biokepi_run_environment.Common.KEDSL.Program.t;`
	`witness : host:Biokepi_run_environment.Common.KEDSL.Host.t -> path:string -> Biokepi_run_environment.Common.KEDSL.unknown_product;`
	`unarchived_directory : string option;`

}

val noop : Biokepi_run_environment.Common.KEDSL.Program.t

val installable_tool : url:string ->
       ?install_program:(path:string ->
                         Biokepi_run_environment.Common.KEDSL.Program.t) ->
       ?init_program:(path:string -> Biokepi_run_environment.Common.KEDSL.Program.t) ->
       witness:(host:Biokepi_run_environment.Common.KEDSL.Host.t ->
                path:string -> Biokepi_run_environment.Common.KEDSL.unknown_product) ->
       ?unarchived_directory:string ->
       Tool_def.t -> installable

val render_installable_tool : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_tools_path:string ->
       installable ->
       Biokepi_run_environment.Machine.Tool.t

val add_to_dollar_path : path:string -> Biokepi_run_environment.Common.KEDSL.Program.t

val make_and_copy_bin : string -> path:string -> Biokepi_run_environment.Common.KEDSL.Program.t

val witness_file : string ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       path:string -> < is_done : Ketrew_pure.Target.Condition.t option >

val witness_list : string list ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       path:string -> < is_done : Ketrew_pure.Target.Condition.t option >

val bwa : installable

val stringtie : installable

val vcftools : installable

val bedtools : installable

val mosaik : installable

val star : installable

val hisat : Tool_def.t -> installable

val kallisto : installable

val samtools : installable

val cufflinks : installable

val somaticsniper : installable

val varscan : installable

val picard : installable

type broad_jar_location = [ `Fail of string | `Scp of string | `Wget of string ]

Mutect (and some other tools) are behind some web-login annoying thing: c.f. <http://www.broadinstitute.org/cancer/cga/mutect_download> So the user of the lib must provide an SSH or HTTP URL (or reimplement the `Tool.t` is some other way).

val get_broad_jar : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_path:string ->
       [< `Fail of 'a & string | `Scp of string | `Wget of string ] ->
       < exists : Ketrew_pure.Target.Condition.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.workflow_node

val mutect_tool : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_tools_path:string ->
       [< `Fail of 'a & string | `Scp of string | `Wget of string ] ->
       Biokepi_run_environment.Machine.Tool.t

val gatk_tool : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_tools_path:string ->
       [< `Fail of 'a & string | `Scp of string | `Wget of string ] ->
       Biokepi_run_environment.Machine.Tool.t

val strelka : installable

Strelka is built from source but does not seem to build on MacOSX.

val virmid : installable

val muse : installable

val default_jar_location : string -> unit -> broad_jar_location

val default_toolkit : run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       host:Biokepi_run_environment.Common.KEDSL.Host.t ->
       install_tools_path:string ->
       ?mutect_jar_location:(unit ->
                             broad_jar_location) ->
       ?gatk_jar_location:(unit ->
                           broad_jar_location) ->
       unit -> Biokepi_run_environment.Machine.Tool.Kit.t