Before the Connectome Mapper 3 BIDS App can be run on a cluster, it first needs to be saved to an Singularity-compatible image file (Please check the Singularity documentation website for more details).
Let's say we want to store Singularity-compatible image file in ~/Softwares/singularity/
:
$ singularity build ~/Softwares/singularity/cmp-.simg docker://sebastientourbier/connectomemapper-bidsapp:
This command will directly download the latest version release of the Docker image from the DockerHub and convert it to a Singularity image.
The following example shows how to call from the terminal the Singularity image of the CMP3 BIDS App to perform both anatomical and diffusion pipelines for sub-01, sub-02 and sub-03 of a BIDS dataset whose root directory is located at ${localDir}
:
$ singularity run --bind ${localDir}:/bids_dir --bind ${localDir}/derivatives:/output_dir \ ~/Softwares/singularity/cmp-v3.0.0-beta-20200227.simg \ /bids_dir /output_dir participant --participant_label 01 02 03 \ --anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini \ --dwi_pipeline_config /bids_dir/code/ref_diffusion_config.ini \ --fs_license /bids_dir/code/license.txt \ --number_of_participants_processed_in_parallel 3
Display a container's metadata:
$ singularity inspect ~/Softwares/singularity/cmp-.simg
Clean cache:
$ singularity cache clean
Created by Sebastien Tourbier - 2020 Mar 04