DeepMedic won't run in singularity container

[Bananahopper]

Describe the bug
When running DeepMedic in a container on a cluster with singularity, I get the following error :

Starting DeepMedic Segmentation.
sh: /work/CaPTk/bin/deepMedicInference: Is a directory
DeepMedic exited with code !=0.
Something went wrong when performing skull-stripping using DeepMedic, please re-try or contact sofware@cbica.upenn.edu.

I get this error when running DeepMedic by itself or through the BraTSPipeline.

To Reproduce
Steps to reproduce the behavior:

1. Pull container from dockerhub with singularity pull docker://cbica/captk:{version}
2. Run container (interactive or not) with command /work/CaPTk/bin/DeepMedic -md /work/CaPTk/bin/../data//deepMedic/saved_models/skullStripping/ -i /output//T1_to_SRI.nii.gz,/output//T1CE_to_SRI.nii.gz,/output//T2_to_SRI.nii.gz,/output//FL_to_SRI.nii.gz -o /output//dmOut_skull/brainMask_SRI.nii.gz
3. See error

Expected behavior
DeepMedic doesn't get stuck and gives an output

Screenshots
If applicable, add screenshots to help explain your problem.

CaPTk Version
azure-latest, but also in latest and all previous containers

HPC:
fedora 8.6

Additional context
In the BraTSPipeline everything before the DeepMedic segmentation runs without issue as intended.

[nicoloesch]

Hi @Bananahopper,

I am sure you have solved the issue by now but I had to deal with it myself today and wanted to provide a little code snippet for everyone that encounters the same issue:

    %post
    # Move DeepMedic out of its directory so the BraTSPipeline works again
    set -e
    BIN_DIR="/work/CaPTk/bin"
    INNER_DIR="$BIN_DIR/deepMedicInference"
    INNER_BIN="$INNER_DIR/deepMedicInference"
    TARGET="$BIN_DIR/deepMedicInference"

    if [ -d "$INNER_DIR" ] && [ -f "$INNER_BIN" ]; then
        echo "[post] Fixing deepMedicInference layout..."
        mv "$INNER_BIN" "$BIN_DIR/.deepMedicInference.tmp"
        rm -rf "$INNER_DIR"
        mv "$BIN_DIR/.deepMedicInference.tmp" "$TARGET"
        chmod +x "$TARGET"
    fi

Make sure to add that to your %post as it moves the binary out of its folder so that the BraTS Pipeline works again.
Hope it helps anyone!

Nico