package bistro

You can search for identifiers within the package.

in-package search v0.2.0

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

Legend:
Library
Module
Module type
Parameter
Class
Class type

Represents a text with special symbols

type t

val dest : t

Symbol representing the location where a workflow is expected to produce its result

val tmp : t

Symbol representing an existing empty directory that can be used as a temporary space for a workflow's execution.

val np : t

Symbol representing the number of cores allocated to the workflow

val mem : t

Symbol representing the memory size allocated to the workflow, in GB.

val exe : t

Symbol representing the path of the current executable, as specified by Sys.argv.(0)

val string : string -> t

A chunk of text

val int : int -> t

Int formatting

val float : float -> t

Float formatting

val path : Path.t -> t

Path formatting

val dep : _ Workflow.t -> t

dep w is interpreted as the path where to find the result of workflow w

val quote : ?using:char -> t -> t

quote ~using:c t surrounds template t with character c

val option : ('a -> t) -> 'a option -> t

option f o is f x if o = Some x and string "" otherwise

val list : ('a -> t) -> ?sep:string -> 'a list -> t

list combinator, optional value of sep is ","

val seq : ?sep:string -> t list -> t

another list combinator, default value for sep is ""

val enum : ('a * string) list -> 'a -> t

combinator for enumerations

val file_dump : t -> t

file_dump t can be used when a command needs a configuration script: at run-time, it will generate a text using t, save it to a path, deterministically chosen as a function of t. Finally the template file_dump t is interpreted as this path.