package bistro

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in-package search v0.2.0

bistro
- Bistro
  - Private
  - Shell_dsl
  - Template_dsl
  - Workflow
  - binary_file
  - bz2
  - directory
  - file
  - gz
  - html
  - pdf
  - png
  - sexp_value
  - svg
  - tar
  - text_file
  - tsv
  - zip
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
    
    index
  - Bowtie2
    
    index
  - ChIPQC
    
    output
  - Cisa
  - DESeq2
    
    table
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Ensembl
  - FastQC
    
    report
  - Fastq
  - Fastq_screen
    
    output
  - Hisat2
  - Htseq
    
    count_tsv
  - Idba
  - Idr
  - Kallisto
    
    abundance_table
    
    index
  - Macs
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_output
    
    broad_peaks
    
    narrow_output
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Picardtools
  - Prokka
  - Quast
  - Samtools
  - Spades
  - Sra_toolkit
  - Srst2
  - Star
  - Subread
    
    count_table
  - Tophat
    
    output
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    output
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    chromosome_sequences
    
    twobit
    
    wig
  - bam
  - bed3
  - bed4
  - bed5
  - bed6
  - fasta
  - fastq
  - gff
  - gff2
  - gff3
  - indexed_bam
  - phred64_fastq
  - sam
  - sanger_fastq
  - solexa_fastq
  - sra
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Docker
  - Eval_thread
    
    Infix
  - Execution_env
  - Execution_trace
  - Local_backend
  - Logger
    
    t
  - Lwt_queue
  - Misc
  - Path
  - Scheduler
    
    Backend
    
    Gc
    
    Make
    
    Backend
  - Shell_command
  - Singularity
  - Task_result
bistro.internals
- Bistro_internals
  - Command
    
    Docker_image
    
    Singularity_image
  - Template
  - Workflow
    
    Any
    
    Map
    
    Set
    
    Table
bistro.multinode
- Bistro_multinode
  - Client
  - Server
bistro.nlp
- Bistro_nlp
  - Stanford_parser
    
    deps
bistro.unix
- Bistro_unix
  - Cmd
bistro.utils
- Bistro_utils

Legend:
Library
Module
Module type
Parameter
Class
Class type

Workflow constructors

val input : ?version:int -> string -> 'a pworkflow

Workflow constructor from an existing path

val shell : 
  ?descr:string ->
  ?mem:int workflow ->
  ?np:int ->
  ?version:int ->
  Shell_dsl.command list ->
  'a path workflow

Constructor for a workflow that execute a shell script. Its main argument is a list of Shell_dsl.cmd values. Other arguments are:

descr description of the workflow, used for logging
mem required memory
np maximum number of cores (could be given less at execution)
version version number, used to force the rebuild of a workflow

val select : directory path workflow -> string list -> 'a path workflow

Constructs a workflow from a directory workflow, by selecting a file in it

val cached_value : 
  ?descr:string ->
  ?np:int ->
  ?mem:int workflow ->
  ?version:int ->
  (unit -> 'a) workflow ->
  'a workflow

val cached_path : 
  ?descr:string ->
  ?np:int ->
  ?mem:int workflow ->
  ?version:int ->
  (string -> unit) workflow ->
  'a path workflow

val pure : id:string -> 'a -> 'a workflow

pure ~id x is a workflow that computes the value x. id should be a string identifying x, like a digest.

val pure_data : 'a -> 'a workflow

Similar to pure, but computes a digest as identifier. Does not work with closures or objects.

val int : int -> int workflow

int i is pure_data i

val string : string -> string workflow

string s is pure_data s

val app : ('a -> 'b) workflow -> 'a workflow -> 'b workflow

Applicative structure

val both : 'a workflow -> 'b workflow -> ('a * 'b) workflow

Applicative structure, useful for parallel binds

val eval_path : 'a path workflow -> string workflow

val eval_paths : 'a path workflow list -> string list workflow

val list : 'a workflow list -> 'a list workflow

val spawn : 
  'a list workflow ->
  f:('a workflow -> 'b workflow) ->
  'b list workflow

val spawn2 : 
  'a list workflow ->
  'b list workflow ->
  f:('a workflow -> 'b workflow -> 'c workflow) ->
  'c list workflow

val glob : 
  ?pattern:string ->
  ?type_selection:[ `File | `Directory ] ->
  directory pworkflow ->
  'a path list workflow