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faskowit / app-multiAtlasTT

brainlife.io version of maTT
MIT License
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App is failing with "module: command not found" #14

Closed soichih closed 3 years ago

soichih commented 3 years ago

Our users are reporting the following error message.

+ module load freesurfer
./main: line 36: module: command not found

We should not use module load freesurfer as it doesn't work on most of our resources, and even if it does, we don't know which version of freesurfer it's pulling (and may change in the future).

I recommend dropping this, and instead always use the freesurfer that comes with a container that you specify.

mohammadhadiaarabi commented 3 years ago

Also, I see this error: Error: (SSH) Channel open failure: open failed

faskowit commented 3 years ago

I thought I fixed this problem with the following line: https://github.com/faskowit/app-multiAtlasTT/blob/master/main#L36

The '||' makes it so the error is caught.

faskowit commented 3 years ago

looks like brainlfie app was pulling from 0.0.6.... I change to 0.0.7. This should fix the issue. Let me know.

faskowit commented 3 years ago

Also, @mohammadhadiarabi I don't really understand that error message without more context. I am not sure how it would relate to the modules command. Hopefully, it goes away in 0.0.7!

soichih commented 3 years ago

Thanks @faskowit 0.0.7 worked.

By the way, it looks like the master branch is more similar to 0.0.6 than 0.0.7. Maybe you should merge the changes you made on 0.0.7 to master?