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