Singularity/Apptainer

Our docker containers are converted to singularity/apptainer containers and stored on Object storage.

Download Singularity Containers

First get an overview of which containers are available as Singularity containers: https://github.com/neurodesk/neurocommand/blob/main/cvmfs/log.txt

curl -s https://raw.githubusercontent.com/neurodesk/neurocommand/main/cvmfs/log.txt

assign the container name to a variable:

export container=itksnap_3.8.0_20201208

Then download the containers. One way is to use CURL:

curl -X GET https://neurocontainers.s3.us-east-2.amazonaws.com/$container.simg -O

Singularity Containers and GPUs

Some of our containers contain GPU-accelerated applications. Here is an example that tests the GPU accelerated program eddy in FSL:

curl -X GET https://neurocontainers.s3.us-east-2.amazonaws.com/fsl_6.0.5.1_20221016.simg -O
git clone https://github.com/neurolabusc/gpu_test.git
singularity shell --nv fsl_6.0.5.1_20221016.simg
cd gpu_test/etest/
bash runme_gpu.sh

Transparent Singularity

The singularity containers can be also be used in combination with our Transparent Singularity Tool, which wraps the executables inside a container to make them easily available for pipelines. More information can be found here:

one example to do this is:

curl -s https://raw.githubusercontent.com/neurodesk/neurocommand/main/cvmfs/log.txt
export container=itksnap_3.8.0_20201208
git clone https://github.com/neurodesk/transparent-singularity ${container}
cd ${container}
./run_transparent_singularity.sh ${container}