Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[BUG] BioContainer STDOut is not attached to FSI, only gets returned when container tasks are finished/aborted #85

Open
kMutagene opened this issue Mar 20, 2020 · 0 comments
Labels
bug project-BioContainers Issues regarding the BioFSharp.BioTools project

Comments

@kMutagene
Copy link
Member

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
@kMutagene kMutagene added bug project-BioContainers Issues regarding the BioFSharp.BioTools project labels Mar 20, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug project-BioContainers Issues regarding the BioFSharp.BioTools project
Projects
None yet
Development

No branches or pull requests

1 participant