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[BUG] BioContainer STDOut is not attached to FSI, only gets returned when container tasks are finished/aborted #3

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@kMutagene

Description

@kMutagene

Describe the bug
BioContainer STDOut is not attached to FSI, only gets returned when container tasks are finished/aborted. This leads to no output until the containerized process is completely finished.

To Reproduce

Here is an example where i wanted to see the progress of a fasterq-dump task in SRATools:


open SRATools

let sraImage = Docker.ImageId "quay.io/biocontainers/sra-tools:2.10.3--pl526haddd2b5_0"

let sraContext = 
    BioContainer.initBcContextWithMountAsync client sraImage  @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data"
    |> Async.RunSynchronously

let FQDOptions =
    [
        FasterQDumpParams.OutDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Testerino"
        FasterQDumpParams.TempDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Testerino\tmp"
        FasterQDumpParams.Split SplitOptions.SplitFiles
        FasterQDumpParams.PrintDetails
        FasterQDumpParams.ShowProgress
    ]

runFasterQDumpOfAccession sraContext FQDOptions "SRR000001"

Output in FSI only gets printed after the whole task is finished:

Expected behavior
STDOut of the container should appear in FSI as produced during the task

to see how it should work, take a look at the output using docker cli:


docker run -it -v C:/Users/kevin/Downloads/CsbScaffold-master/MetaIndexing_New/data:/data f9876632ae1e

/ # cd data
/data # fasterq-dump -O ./Testerino -t ./Testerino/tmp --split-files -x -p SRR000001

OS and framework information (please complete the following information):

  • OS: Windows 10
  • OS Version 1909
  • .Net core SDK version 3.1.102
  • Docker Desktop Community 2.2.0.4 (43472) stable

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