: sig

(** Download reference-genormes (& associated data) with Ketrew *)

open Biokepi_run_environment type pull_function =   toolkit:Machine.Tool.Kit.t ->   host:Common.KEDSL.Host.t ->   run_program:Machine.Make_fun.t ->   destination_path:string -> Reference_genome.t val pull_b37 : pull_function val pull_b37decoy : pull_function val pull_b38 : pull_function val pull_hg18 : pull_function val pull_hg19 : pull_function val pull_mm10 : pull_function val default_genome_providers : (string * pull_function) list val get_reference_genome : string -> pull_function end  = struct open Biokepi_run_environment open Common open Workflow_utilities.Download (* All the wget* functions *) module Vcftools = Workflow_utilities.Vcftools let of_specification     ~toolkit ~host ~run_program ~destination_path specification =   let open Reference_genome in   let {     Specification.     name;     ensembl;     species;     metadata;     fasta;     dbsnp;     known_indels;     cosmic;     exome_gtf; (* maybe desrves a better name? *)     cdna;     whess;     major_contigs;   } = specification in   let dest_file f = destination_path // name // f in   let rec compile_location filename =     function     | `Url url (* Right now, `wget_gunzip` is clever enough to not gunzip *)     | `Gunzip `Url url ->       Workflow_utilities.Download.wget_gunzip         ~host ~run_program ~destination:(dest_file filename) url     | `Bunzip2 `Url url ->       Workflow_utilities.Download.wget_bunzip2         ~host ~run_program ~destination:(dest_file filename) url     | `Vcf_concat l ->       let vcfs =         List.map ~f:(fun (n, loc) -> compile_location n loc) l       in       let vcftools =         Machine.Tool.Kit.get_exn toolkit Machine.Tool.Default.vcftools in       let concated =         let tmp_vcf =           dest_file (Filename.chop_extension filename ^ "-cat.vcf") in         Vcftools.vcf_concat_no_machine           ~make_product:(fun p -> KEDSL.single_file p ~host)           ~host ~vcftools ~run_program ~final_vcf:tmp_vcf vcfs in       let sorted =         let final_vcf_path = dest_file filename in         Vcftools.vcf_sort_no_machine           ~make_product:(fun p -> KEDSL.single_file p ~host)           ~host ~vcftools ~run_program           ~src:concated ~dest:final_vcf_path () in       sorted     | other ->       failwithf "Reference_genome.compile_location this kind of location is not yet implemented"   in   let compile_location_opt filename =     Option.map ~f:(compile_location filename) in   create specification     (compile_location (name ^ ".fasta") fasta)     ?cosmic:(compile_location_opt "cosmic.vcf" cosmic)     ?dbsnp:(compile_location_opt "dbsnp.vcf" dbsnp)     ?known_indels:(compile_location_opt "known_indels.vcf" dbsnp)     ?gtf:(compile_location_opt "transcripts.gtf" exome_gtf)     ?cdna:(compile_location_opt "cdns-all.fa" cdna)     ?whess:(compile_location_opt "whess.sqlite" whess) type pull_function =   toolkit:Machine.Tool.Kit.t ->   host:Common.KEDSL.Host.t ->   run_program:Machine.Make_fun.t ->   destination_path:string -> Reference_genome.t let pull_b37 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.b37 let pull_b37decoy ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.b37decoy let pull_b38 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.b38 let pull_hg38 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.hg38 let pull_hg19 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.hg19 let pull_hg18 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.hg18 let pull_mm10 ~toolkit ~host ~(run_program : Machine.Make_fun.t) ~destination_path =   of_specification ~toolkit ~host ~run_program ~destination_path     Reference_genome.Specification.Default.mm10 let default_genome_providers = [   Reference_genome.Specification.Default.Name.b37, pull_b37;   Reference_genome.Specification.Default.Name.b37decoy, pull_b37decoy;   Reference_genome.Specification.Default.Name.b38, pull_b38;   Reference_genome.Specification.Default.Name.hg38, pull_hg38;   Reference_genome.Specification.Default.Name.hg18, pull_hg18;   Reference_genome.Specification.Default.Name.hg19, pull_hg19;   Reference_genome.Specification.Default.Name.mm10, pull_mm10; ] let get_reference_genome name =   match List.find default_genome_providers ~f:(fun (a, _) -> a = name) with   | Some (_, pull) -> pull   | None -> failwithf "Cannot find the reference genorme called %S" name                end