jpvaldes / cbbs-imaging-container-mriqc Goto Github PK

Hi

When building the singularity image myself, I was puzzled by the entrypoint of the resulting mriqc container. I now believe that such behaviour is fully intended by singularity, but following the suggestion from @bpoldrack I am describing the situation below, hoping it might come useful to you.

I am using singularity-2.4 via vagrant and virtualbox (on MacOS).

Specifically, I noticed that if I build the container using:
singularity build mriqc.img docker://poldracklab/fmriprep,
the runscript of such image (checked by singularity inspect --runscript) gets automatically set to exec "/usr/local/miniconda/bin/mriqc".

As a result, it cannot be used as an executable directly, but has to be launched using singularity exec ....

However, I can also use the following build specification file (saved in the example below as Singularity) to change the runscript ($@ ensures that arguments are passed along from the user):

Bootstrap: docker
From: poldracklab/mriqc:0.10.4

%runscript

    /usr/local/miniconda/bin/mriqc $@

The image can then be built by running sudo singularity build mriqc.img Singularity.
I can execute this image directly: ./mriqc.img bids-root/ output-folder/ participant

I find the latter behaviour more natural -- but in the end, using it would require changing the datalad wrapper, so I leave the decision to you.

Relevant Singularity docs:

• Singularity and Docker
• Defining the runscript