package bistro

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package bistro

bistro
- Bistro
  - Command
  - EDSL
  - Path
  - Std
    
    Unix_tools
    
    binary_file
    
    bz2
    
    directory
    
    file
    
    gz
    
    html
    
    marshalled_value
    
    pdf
    
    png
    
    sexp_value
    
    svg
    
    tar
    
    text_file
    
    tsv
    
    zip
  - Template
  - U
  - Workflow
  - directory
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - ChIPQC
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Defs
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    gff2
    
    gff3
    
    sam
    
    sra
  - Deseq2
    
    table
  - Ensembl
  - FastQC
  - Fastq
  - Fastq_screen
  - Htseq
    
    count_tsv
  - Jaspar
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_peaks
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Misc
    
    Infix
  - Prokka
  - Samtools
  - Spades
  - Sra
  - Sra_toolkit
  - Srst2
  - Std
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    sam
    
    sra
  - Tophat
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    twobit
    
    wig
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Lwt_utils
  - Scheduler
    
    DAG
    
    logger
    
    logger
  - Task
bistro.tdag
- Bistro_tdag
  - Tdag
    
    Make
    
    D
    
    Allocator
    
    Task
    
    Thread
    
    logger
  - Tdag_sig
    
    Domain
    
    Allocator
    
    Task
    
    Thread
    
    S
    
    logger
bistro.utils
- Bistro_utils
  - Console_logger
  - Dot_output
  - Html_logger
  - Logger
  - Repo
  - Term
    
    Syntax
    
    Let_syntax

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Module
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Class type

module DAG : Bistro_tdag.Tdag_sig.S with type task = Task.t

type time = float

type event =

| Init of {
1. dag : DAG.t;
2. needed : Task.t list;
3. already_done : Task.t list;
}
| Task_ready of Task.t
| Task_started of Task.t * Allocator.resource
| Task_ended of Task.result
| Task_skipped of Task.t * [ `Done_already | `Missing_dep | `Allocation_error of string ]

class type logger = object ... end

type trace =

| Run of {
1. ready : time;
2. start : time;
3. end_ : time;
4. outcome : Task.result;
}
| Skipped of [ `Done_already | `Missing_dep | `Allocation_error of string ]

type dry_run =

| Dry_run of {
1. nb_tasks : int;
2. nb_goals : int;
3. status : (Task.t * [ `TODO | `DONE ]) list;
4. simulation : Task.t list;
}

val compile : 
  Bistro.any_workflow list ->
  DAG.t * Task.t list * Core_kernel.String.Set.t

val run : 
  ?logger:logger ->
  ?goals:Task.t list ->
  Task.config ->
  Allocator.t ->
  DAG.t ->
  trace Core_kernel.String.Map.t Lwt.t

val dry_run : ?goals:Task.t list -> Task.config -> DAG.t -> dry_run Lwt.t

val clean_run : Task.config -> DAG.t -> unit Lwt.t