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 ->
       ?archive_is_directory:bool ->
       string -> 'a Biokepi_run_environment.Common.KEDSL.workflow_node

val git_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 ->
       repository:string ->
       recursive:bool ->
       Biokepi_run_environment.Machine.Tool.Definition.t ->
       'a Biokepi_run_environment.Common.KEDSL.workflow_node

module Tool_def: Biokepi_run_environment.Machine.Tool.Definition

module Installable_tool: sig .. end

module Git_installable_tool: sig .. end

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_tool.t

val freebayes : Git_installable_tool.t

val sambamba : Installable_tool.t

val stringtie : Installable_tool.t

val vcftools : Installable_tool.t

val bedtools : Installable_tool.t

val mosaik : Installable_tool.t

val star : Installable_tool.t

val hisat : Tool_def.t -> Installable_tool.t

val kallisto : Installable_tool.t

val samtools : Installable_tool.t

val cufflinks : Installable_tool.t

val somaticsniper : Installable_tool.t

val varscan : Installable_tool.t

val picard : Installable_tool.t

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 ->
       Biokepi_run_environment.Workflow_utilities.Download.tool_file_location ->
       < 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.product
       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 ->
       Biokepi_run_environment.Workflow_utilities.Download.tool_file_location ->
       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 ->
       Biokepi_run_environment.Workflow_utilities.Download.tool_file_location ->
       Biokepi_run_environment.Machine.Tool.t

val strelka : Installable_tool.t

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

val virmid : Installable_tool.t

val muse : Installable_tool.t

val fastqc : Installable_tool.t

val samblaster : Installable_tool.t

val default_tool_location : string ->
       unit ->
       Biokepi_run_environment.Workflow_utilities.Download.tool_file_location

val default_netmhc_locations : unit -> Biokepi_environment_setup.Netmhc.netmhc_file_locations

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 ->
                             Biokepi_run_environment.Workflow_utilities.Download.tool_file_location) ->
       ?gatk_jar_location:(unit ->
                           Biokepi_run_environment.Workflow_utilities.Download.tool_file_location) ->
       ?netmhc_tool_locations:(unit ->
                               Biokepi_environment_setup.Netmhc.netmhc_file_locations) ->
       unit -> Biokepi_run_environment.Machine.Tool.Kit.t