Trying to run a series of bash commands on Windows but failed

[citystrawman]

Hi, I am trying to run a series of bash commands on Windows but failed.
the bash commands contains 3 steps, and I checked its validity by typing the commands manually:

1. I started bash by typing bash into powershell;
2. after entering bash, I ran the 3 commands in one round by concatenating the 3 commands using ;, the result is as follows:
   

In this sense, I think CliWrap could run these commands, and I implemented is as follows:

var result = await Cli.Wrap(bashPath)
    .WithArguments(args => args
    .Add($"export FREESURFER_HOME={sourceScriptDirWsl}")
    .Add(" ; ")
    .Add("source $FREESURFER_HOME/SetUpFreeSurfer.sh")
    .Add(" ; ")
    .Add(stripPathWsl)
    .Add("-i")
    .Add(inputPathWsl)
    .Add("-o")
    .Add(outputPathWsl)
    ).ExecuteBufferedAsync(cts.Token);

However, when running this code, I got errors:

Command execution failed, see the inner exception for details.

Standard error:
/bin/bash: export FREESURFER_HOME=/mnt/e/MRI-WPF/AlphaBrain/bin/Debug/net8.0-windows/Commands/freesurfer: No such file or directory

and the command is as follows::

Command = {C:\windows\system32\bash.exe "export FREESURFER_HOME=/mnt/e/freesurfer" " ; " "source $FREESURFER_HOME/SetUpFreeSurfer.sh" " ; " /mnt/e/freesurfer/bin/mri_synthstrip -i /mnt/e/T1_t1_mprage.nii -o /mnt/e/stripped.nii}

I am not sure what is the problem here. I am not sure if CliWrap could not handle multiple sequenced command, or whether the environment variable FREESURFER_HOME could not be regonized in string format?
I appreciate if you could help me solving this issue. Thank you!

[citystrawman]

Now, I even tried hard coding:

string argstr = "export FREESURFER_HOME=/mnt/e/freesurfer ; source $FREESURFER_HOME/SetUpFreeSurfer.sh ; /mnt/e/freesurfer/bin/mri_synthstrip -i /mnt/e/T1_t1_mprage.nii -o /mnt/e/strippedBash.nii";

var result = await Cli.Wrap(bashPath)
    .WithArguments(args => args
    .Add(argstr)
    ).ExecuteBufferedAsync(cts.Token);

but still got same errors. However, if I paste the argstr manually into bash, it runs successfully.

[Tyrrrz]

I'm pretty sure you need to do bash -c "<your command>", so something like this:

var result = await Cli.Wrap(bashPath)
    .WithArguments(args => args
        .Add("-c")
        .Add(new ArgumentsBuilder()
		    .Add($"export FREESURFER_HOME={sourceScriptDirWsl}")
		    .Add(" ; ")
		    .Add("source $FREESURFER_HOME/SetUpFreeSurfer.sh")
		    .Add(" ; ")
		    .Add(stripPathWsl)
		    .Add("-i")
		    .Add(inputPathWsl)
		    .Add("-o")
		    .Add(outputPathWsl)
            .Build()
       )
    ).ExecuteBufferedAsync(cts.Token);

[citystrawman]

Hi, I tried this method, but CliWrap still reports No such file or directory when it executes at $"export FREESURFER_HOME={sourceScriptDirWsl}"

the above screenshots are error info and the directory that I need to export as FREESURFER_HOME

and here's my CliWrap code.

[Tyrrrz]

Can you try this instead:

var result = await Cli.Wrap(bashPath)
    .WithArguments(args => args
        .Add("-c")
        .Add(new ArgumentsBuilder()
		    .Add("source $FREESURFER_HOME/SetUpFreeSurfer.sh")
		    .Add(" ; ")
		    .Add(stripPathWsl)
		    .Add("-i")
		    .Add(inputPathWsl)
		    .Add("-o")
		    .Add(outputPathWsl)
            .Build()
        )
    ).WithEnvironmentVariables(env => env
        .Set("FREESURFER_HOME", sourceScriptDirWsl)
    )
).ExecuteBufferedAsync(cts.Token);

[citystrawman]

Thank you! I found that by using new ArgumentsBuilder() the string has double quotes, thus I just use hard-coded string and now it works.

Thank you so much!