CuBIDS on Bianca

https://cubids.readthedocs.io/en/latest/

Running CuBIDS on Bianca

Make sure you have the 'cubids.sif' container somewhere in your project folder.

#cd to where is your data
cd ...

# Start a shell in the container. Replace with the full path.
apptainer shell /full_path_to/cubids.sif

# running the CuBIDS tool
cubids -h

It is highly recommended to configure Git before using DataLad. Set both 'user.name' and 'user.email' configuration variables.
usage: cubids [-h] [-v]
              {validate,bids-version,sidecar-merge,group,apply,purge,add-nifti-info,copy-exemplars,undo,datalad-save,print-metadata-fields,remove-metadata-fields}
              ...

# bids-validator 
bids-validator -h

Usage:   bids-validator <dataset_directory>
Version: 2.0.5
Description:
  This tool checks if a dataset in a given directory is compatible with the Brain Imaging Data Structure specification. To learn more about
  Brain Imaging Data Structure visit http://bids.neuroimaging.io
Options:

Building CuBIDS container

Copy the following two files in a folder.

cubids.def

BootStrap: docker                           
From: mambaorg/micromamba:1.5.10-noble      
                                            
%files                                      
  conda.yml /scratch/conda.yml              
                                            
%environment                                
  export LC_ALL=C.utf8                      
  export PYTHONNOUSERSITE=True              
  export DEBIAN_FRONTEND=noninteractive     
  export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                                            
%post                                       
  export LC_ALL=C.utf8                      
  export PYTHONNOUSERSITE=True                                                                                                             
  export DEBIAN_FRONTEND=noninteractive
  export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
 
  micromamba install -y -n base -f /scratch/conda.yml
  micromamba install -y -n base conda-forge::procps-ng
  micromamba env export --name base --explicit > environment.lock
  echo ">> CONDA_LOCK_START"                
  cat environment.lock                      
  echo "<< CONDA_LOCK_END"                  
  micromamba clean -a -y                    
                                            
  mkdir -p /installs && cd /installs        
  deno compile -ERWN -o bids-validator jsr:@bids/validator
  mv bids-validator /usr/bin                
                                            
%runscript                                  
#!/bin/sh                                   
  if command -v $SINGULARITY_NAME > /dev/null 2> /dev/null; then
    exec $SINGULARITY_NAME "$@"             
  else                                      
    echo "# ERROR !!! Command $SINGULARITY_NAME not found in the container"
  fi

conda.yml

channels:
- conda-forge
- bioconda
dependencies:
- conda-forge::python=3.12
- conda-forge::deno
- conda-forge::git
- conda-forge::p7zip
- pip
- pip:
  - cubids

Building Singularity/Apptainer container on Berzelius

https://www.nsc.liu.se/support/systems/berzelius-software/berzelius-apptainer/#building-apptainer-images

apptainer build --fakeroot cubids.sif cubids.def

Copy the new cubids.sif file on Bianca. You can chose to replace the old or keep it with under different name.

Contacts:

• Pavlin Mitev
• UPPMAX
• AE@UPPMAX - related documentation

tags: UPPMAX,CuBIDS